LinkDB: 2BVJ 2C6H 2C7X 2CD8
Original site: 2BVJ 2C6H 2C7X 2CD8
HEADER OXIDOREDUCTASE 28-JUN-05 2BVJ TITLE LIGAND-FREE STRUCTURE OF CYTOCHROME P450 PIKC (CYP107L1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 MONOOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYTOCHROME P450 PIKC CYP107L1, CYTOCHROME P450 HYDROXYLASE COMPND 5 PIKC; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE; SOURCE 3 ORGANISM_TAXID: 54571; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CYTOCHROME P450, PIKC, CYP107L1, MACROLIDE MONOOXYGENASE, ANTIBIOTIC KEYWDS 2 BIOSYNTHESIS, HEME, IRON, METAL-BINDING, MONOOXYGENASE, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.H.SHERMAN,S.LI,L.V.YERMALITSKAYA,Y.KIM,J.A.SMITH,M.R.WATERMAN, AUTHOR 2 L.M.PODUST REVDAT 4 13-DEC-23 2BVJ 1 LINK REVDAT 3 24-FEB-09 2BVJ 1 VERSN REVDAT 2 06-SEP-06 2BVJ 1 JRNL REVDAT 1 03-JUL-06 2BVJ 0 JRNL AUTH D.H.SHERMAN,S.LI,L.V.YERMALITSKAYA,Y.KIM,J.A.SMITH, JRNL AUTH 2 M.R.WATERMAN,L.M.PODUST JRNL TITL THE STRUCTURAL BASIS FOR SUBSTRATE ANCHORING, ACTIVE SITE JRNL TITL 2 SELECTIVITY, AND PRODUCT FORMATION BY P450 PIKC FROM JRNL TITL 3 STREPTOMYCES VENEZUELAE. JRNL REF J.BIOL.CHEM. V. 281 26289 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16825192 JRNL DOI 10.1074/JBC.M605478200 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 65959.720 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 53812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5448 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6800 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 806 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6046 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 315 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.53000 REMARK 3 B22 (A**2) : -1.73000 REMARK 3 B33 (A**2) : 9.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.50000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.940 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.810 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.790 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 51.38 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISORDERED REGIONS WERE OMMITED FROM REMARK 3 THE STRUCTURE REMARK 4 REMARK 4 2BVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1290024623. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI (220) DOUBLE CRYSTAL REMARK 200 OPTICS : SAGITTAL FOCUSING CRYSTAL AND REMARK 200 VERTICALLY FOCUSING DOUBLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55910 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1OXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000; 0.1 M HEPES, PH 7.5; 0.5 REMARK 280 MM DTT, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 109.09500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.08550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 109.09500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.08550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 THR A 4 REMARK 465 GLN A 5 REMARK 465 GLN A 6 REMARK 465 GLY A 7 REMARK 465 THR A 8 REMARK 465 THR A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 PRO A 12 REMARK 465 PRO A 13 REMARK 465 ARG A 409 REMARK 465 GLU A 410 REMARK 465 ALA A 411 REMARK 465 GLY A 412 REMARK 465 ARG A 413 REMARK 465 ARG A 414 REMARK 465 THR A 415 REMARK 465 GLY A 416 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 ARG B 3 REMARK 465 THR B 4 REMARK 465 GLN B 5 REMARK 465 GLN B 6 REMARK 465 GLY B 7 REMARK 465 THR B 8 REMARK 465 THR B 9 REMARK 465 ALA B 10 REMARK 465 THR B 82 REMARK 465 GLU B 83 REMARK 465 ALA B 84 REMARK 465 GLU B 85 REMARK 465 ALA B 86 REMARK 465 ALA B 87 REMARK 465 ARG B 409 REMARK 465 GLU B 410 REMARK 465 ALA B 411 REMARK 465 GLY B 412 REMARK 465 ARG B 413 REMARK 465 ARG B 414 REMARK 465 THR B 415 REMARK 465 GLY B 416 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 GLU A 83 CG CD OE1 OE2 REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 180 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 182 CG OD1 OD2 REMARK 470 GLU A 300 CG CD OE1 OE2 REMARK 470 GLY A 408 CA C O REMARK 470 ARG B 75 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 81 CG CD1 CD2 REMARK 470 LEU B 88 CG CD1 CD2 REMARK 470 ASN B 89 CG OD1 ND2 REMARK 470 LYS B 105 CG CD CE NZ REMARK 470 PHE B 178 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 186 CG CD OE1 NE2 REMARK 470 GLN B 188 CG CD OE1 NE2 REMARK 470 THR B 189 OG1 CG2 REMARK 470 MET B 191 CG SD CE REMARK 470 GLN B 208 CG CD OE1 NE2 REMARK 470 ASP B 209 CG OD1 OD2 REMARK 470 GLU B 223 CG CD OE1 OE2 REMARK 470 GLY B 408 CA C O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 C1 BME A 1409 C1 BME A 1409 2556 1.58 REMARK 500 C1 BME B 1409 C1 BME B 1409 2557 1.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 94 48.10 -97.61 REMARK 500 LEU A 148 -55.69 -145.80 REMARK 500 VAL A 179 -74.39 -54.24 REMARK 500 PHE A 180 71.24 -111.24 REMARK 500 ASP A 183 138.64 -171.85 REMARK 500 ASP A 209 50.15 -107.67 REMARK 500 LEU A 228 108.30 -161.26 REMARK 500 HIS A 245 -34.44 -154.36 REMARK 500 CYS A 354 115.42 -32.71 REMARK 500 TRP A 405 37.95 -149.06 REMARK 500 LEU B 148 -56.76 -141.50 REMARK 500 VAL B 179 -47.75 -142.35 REMARK 500 PHE B 180 68.36 -113.49 REMARK 500 ALA B 187 -79.03 -43.70 REMARK 500 GLN B 208 162.02 175.00 REMARK 500 HIS B 245 -80.21 -95.62 REMARK 500 GLU B 287 59.48 -140.35 REMARK 500 ASN B 392 118.36 177.64 REMARK 500 TRP B 405 25.57 -141.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1408 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 354 SG REMARK 620 2 HEM A1408 NA 96.7 REMARK 620 3 HEM A1408 NB 84.0 91.4 REMARK 620 4 HEM A1408 NC 81.9 178.3 89.5 REMARK 620 5 HEM A1408 ND 98.2 89.1 177.7 90.1 REMARK 620 6 HOH A2087 O 167.1 89.6 84.6 92.0 93.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B1408 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 354 SG REMARK 620 2 HEM B1408 NA 99.3 REMARK 620 3 HEM B1408 NB 87.4 91.3 REMARK 620 4 HEM B1408 NC 83.5 177.1 88.7 REMARK 620 5 HEM B1408 ND 96.7 89.7 175.6 90.0 REMARK 620 6 HOH B2101 O 167.7 80.4 80.4 96.8 95.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A1409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A1410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B1409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C6H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2C7X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NARBOMYCIN-BOUND CYTOCHROME P450 PIKC REMARK 900 (CYP107L1) REMARK 900 RELATED ID: 2CA0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2CD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN REMARK 999 CLEAVAGE SITE ARE FROM THE CLONING VECTOR PET28A DBREF 2BVJ A -19 0 PDB 2BVJ 2BVJ -19 0 DBREF 2BVJ A 1 416 UNP O87605 O87605_9ACTO 1 416 DBREF 2BVJ B -19 0 PDB 2BVJ 2BVJ -19 0 DBREF 2BVJ B 1 416 UNP O87605 O87605_9ACTO 1 416 SEQRES 1 A 436 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 436 LEU VAL PRO ARG GLY SER HIS MET ARG ARG THR GLN GLN SEQRES 3 A 436 GLY THR THR ALA SER PRO PRO VAL LEU ASP LEU GLY ALA SEQRES 4 A 436 LEU GLY GLN ASP PHE ALA ALA ASP PRO TYR PRO THR TYR SEQRES 5 A 436 ALA ARG LEU ARG ALA GLU GLY PRO ALA HIS ARG VAL ARG SEQRES 6 A 436 THR PRO GLU GLY ASP GLU VAL TRP LEU VAL VAL GLY TYR SEQRES 7 A 436 ASP ARG ALA ARG ALA VAL LEU ALA ASP PRO ARG PHE SER SEQRES 8 A 436 LYS ASP TRP ARG ASN SER THR THR PRO LEU THR GLU ALA SEQRES 9 A 436 GLU ALA ALA LEU ASN HIS ASN MET LEU GLU SER ASP PRO SEQRES 10 A 436 PRO ARG HIS THR ARG LEU ARG LYS LEU VAL ALA ARG GLU SEQRES 11 A 436 PHE THR MET ARG ARG VAL GLU LEU LEU ARG PRO ARG VAL SEQRES 12 A 436 GLN GLU ILE VAL ASP GLY LEU VAL ASP ALA MET LEU ALA SEQRES 13 A 436 ALA PRO ASP GLY ARG ALA ASP LEU MET GLU SER LEU ALA SEQRES 14 A 436 TRP PRO LEU PRO ILE THR VAL ILE SER GLU LEU LEU GLY SEQRES 15 A 436 VAL PRO GLU PRO ASP ARG ALA ALA PHE ARG VAL TRP THR SEQRES 16 A 436 ASP ALA PHE VAL PHE PRO ASP ASP PRO ALA GLN ALA GLN SEQRES 17 A 436 THR ALA MET ALA GLU MET SER GLY TYR LEU SER ARG LEU SEQRES 18 A 436 ILE ASP SER LYS ARG GLY GLN ASP GLY GLU ASP LEU LEU SEQRES 19 A 436 SER ALA LEU VAL ARG THR SER ASP GLU ASP GLY SER ARG SEQRES 20 A 436 LEU THR SER GLU GLU LEU LEU GLY MET ALA HIS ILE LEU SEQRES 21 A 436 LEU VAL ALA GLY HIS GLU THR THR VAL ASN LEU ILE ALA SEQRES 22 A 436 ASN GLY MET TYR ALA LEU LEU SER HIS PRO ASP GLN LEU SEQRES 23 A 436 ALA ALA LEU ARG ALA ASP MET THR LEU LEU ASP GLY ALA SEQRES 24 A 436 VAL GLU GLU MET LEU ARG TYR GLU GLY PRO VAL GLU SER SEQRES 25 A 436 ALA THR TYR ARG PHE PRO VAL GLU PRO VAL ASP LEU ASP SEQRES 26 A 436 GLY THR VAL ILE PRO ALA GLY ASP THR VAL LEU VAL VAL SEQRES 27 A 436 LEU ALA ASP ALA HIS ARG THR PRO GLU ARG PHE PRO ASP SEQRES 28 A 436 PRO HIS ARG PHE ASP ILE ARG ARG ASP THR ALA GLY HIS SEQRES 29 A 436 LEU ALA PHE GLY HIS GLY ILE HIS PHE CYS ILE GLY ALA SEQRES 30 A 436 PRO LEU ALA ARG LEU GLU ALA ARG ILE ALA VAL ARG ALA SEQRES 31 A 436 LEU LEU GLU ARG CYS PRO ASP LEU ALA LEU ASP VAL SER SEQRES 32 A 436 PRO GLY GLU LEU VAL TRP TYR PRO ASN PRO MET ILE ARG SEQRES 33 A 436 GLY LEU LYS ALA LEU PRO ILE ARG TRP ARG ARG GLY ARG SEQRES 34 A 436 GLU ALA GLY ARG ARG THR GLY SEQRES 1 B 436 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 436 LEU VAL PRO ARG GLY SER HIS MET ARG ARG THR GLN GLN SEQRES 3 B 436 GLY THR THR ALA SER PRO PRO VAL LEU ASP LEU GLY ALA SEQRES 4 B 436 LEU GLY GLN ASP PHE ALA ALA ASP PRO TYR PRO THR TYR SEQRES 5 B 436 ALA ARG LEU ARG ALA GLU GLY PRO ALA HIS ARG VAL ARG SEQRES 6 B 436 THR PRO GLU GLY ASP GLU VAL TRP LEU VAL VAL GLY TYR SEQRES 7 B 436 ASP ARG ALA ARG ALA VAL LEU ALA ASP PRO ARG PHE SER SEQRES 8 B 436 LYS ASP TRP ARG ASN SER THR THR PRO LEU THR GLU ALA SEQRES 9 B 436 GLU ALA ALA LEU ASN HIS ASN MET LEU GLU SER ASP PRO SEQRES 10 B 436 PRO ARG HIS THR ARG LEU ARG LYS LEU VAL ALA ARG GLU SEQRES 11 B 436 PHE THR MET ARG ARG VAL GLU LEU LEU ARG PRO ARG VAL SEQRES 12 B 436 GLN GLU ILE VAL ASP GLY LEU VAL ASP ALA MET LEU ALA SEQRES 13 B 436 ALA PRO ASP GLY ARG ALA ASP LEU MET GLU SER LEU ALA SEQRES 14 B 436 TRP PRO LEU PRO ILE THR VAL ILE SER GLU LEU LEU GLY SEQRES 15 B 436 VAL PRO GLU PRO ASP ARG ALA ALA PHE ARG VAL TRP THR SEQRES 16 B 436 ASP ALA PHE VAL PHE PRO ASP ASP PRO ALA GLN ALA GLN SEQRES 17 B 436 THR ALA MET ALA GLU MET SER GLY TYR LEU SER ARG LEU SEQRES 18 B 436 ILE ASP SER LYS ARG GLY GLN ASP GLY GLU ASP LEU LEU SEQRES 19 B 436 SER ALA LEU VAL ARG THR SER ASP GLU ASP GLY SER ARG SEQRES 20 B 436 LEU THR SER GLU GLU LEU LEU GLY MET ALA HIS ILE LEU SEQRES 21 B 436 LEU VAL ALA GLY HIS GLU THR THR VAL ASN LEU ILE ALA SEQRES 22 B 436 ASN GLY MET TYR ALA LEU LEU SER HIS PRO ASP GLN LEU SEQRES 23 B 436 ALA ALA LEU ARG ALA ASP MET THR LEU LEU ASP GLY ALA SEQRES 24 B 436 VAL GLU GLU MET LEU ARG TYR GLU GLY PRO VAL GLU SER SEQRES 25 B 436 ALA THR TYR ARG PHE PRO VAL GLU PRO VAL ASP LEU ASP SEQRES 26 B 436 GLY THR VAL ILE PRO ALA GLY ASP THR VAL LEU VAL VAL SEQRES 27 B 436 LEU ALA ASP ALA HIS ARG THR PRO GLU ARG PHE PRO ASP SEQRES 28 B 436 PRO HIS ARG PHE ASP ILE ARG ARG ASP THR ALA GLY HIS SEQRES 29 B 436 LEU ALA PHE GLY HIS GLY ILE HIS PHE CYS ILE GLY ALA SEQRES 30 B 436 PRO LEU ALA ARG LEU GLU ALA ARG ILE ALA VAL ARG ALA SEQRES 31 B 436 LEU LEU GLU ARG CYS PRO ASP LEU ALA LEU ASP VAL SER SEQRES 32 B 436 PRO GLY GLU LEU VAL TRP TYR PRO ASN PRO MET ILE ARG SEQRES 33 B 436 GLY LEU LYS ALA LEU PRO ILE ARG TRP ARG ARG GLY ARG SEQRES 34 B 436 GLU ALA GLY ARG ARG THR GLY HET HEM A1408 43 HET BME A1409 4 HET DTT A1410 8 HET HEM B1408 43 HET BME B1409 4 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM BME BETA-MERCAPTOETHANOL HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETSYN HEM HEME HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 BME 2(C2 H6 O S) FORMUL 5 DTT C4 H10 O2 S2 FORMUL 8 HOH *315(H2 O) HELIX 1 1 LEU A 20 ASP A 27 1 8 HELIX 2 2 PRO A 28 GLY A 39 1 12 HELIX 3 3 GLY A 57 ASP A 67 1 11 HELIX 4 4 ASP A 73 SER A 77 5 5 HELIX 5 5 THR A 82 ASN A 89 1 8 HELIX 6 6 PRO A 98 ALA A 108 1 11 HELIX 7 7 ARG A 109 PHE A 111 5 3 HELIX 8 8 THR A 112 LEU A 118 1 7 HELIX 9 9 LEU A 119 LEU A 135 1 17 HELIX 10 10 LEU A 144 LEU A 148 1 5 HELIX 11 11 TRP A 150 LEU A 161 1 12 HELIX 12 12 PRO A 164 ASP A 167 5 4 HELIX 13 13 ARG A 168 PHE A 180 1 13 HELIX 14 14 ASP A 183 ARG A 206 1 24 HELIX 15 15 ASP A 212 ASP A 224 1 13 HELIX 16 16 THR A 229 ALA A 243 1 15 HELIX 17 17 HIS A 245 SER A 261 1 17 HELIX 18 18 HIS A 262 ASP A 272 1 11 HELIX 19 19 LEU A 275 GLY A 288 1 14 HELIX 20 20 VAL A 318 HIS A 323 1 6 HELIX 21 21 GLY A 356 CYS A 375 1 20 HELIX 22 22 SER A 383 LEU A 387 5 5 HELIX 23 23 GLY B 18 LEU B 20 5 3 HELIX 24 24 GLY B 21 ASP B 27 1 7 HELIX 25 25 PRO B 28 GLY B 39 1 12 HELIX 26 26 GLY B 57 ASP B 67 1 11 HELIX 27 27 ASP B 73 SER B 77 5 5 HELIX 28 28 ASN B 91 SER B 95 5 5 HELIX 29 29 PRO B 98 ARG B 109 1 12 HELIX 30 30 THR B 112 LEU B 119 1 8 HELIX 31 31 LEU B 119 LEU B 135 1 17 HELIX 32 32 LEU B 144 LEU B 148 1 5 HELIX 33 33 TRP B 150 LEU B 161 1 12 HELIX 34 34 PRO B 164 PHE B 178 1 15 HELIX 35 35 ASP B 183 ARG B 206 1 24 HELIX 36 36 ASP B 212 THR B 220 1 9 HELIX 37 37 THR B 229 HIS B 245 1 17 HELIX 38 38 HIS B 245 SER B 261 1 17 HELIX 39 39 HIS B 262 ASP B 272 1 11 HELIX 40 40 LEU B 275 GLY B 288 1 14 HELIX 41 41 VAL B 318 HIS B 323 1 6 HELIX 42 42 GLY B 356 CYS B 375 1 20 HELIX 43 43 SER B 383 LEU B 387 5 5 SHEET 1 AA 4 LEU A 15 ASP A 16 0 SHEET 2 AA 4 ALA A 41 ARG A 45 1 O ARG A 43 N LEU A 15 SHEET 3 AA 4 GLU A 51 VAL A 55 -1 O VAL A 52 N VAL A 44 SHEET 4 AA 4 VAL A 315 VAL A 317 1 O LEU A 316 N VAL A 55 SHEET 1 AB 2 PHE A 70 SER A 71 0 SHEET 2 AB 2 PHE A 297 PRO A 298 -1 O PHE A 297 N SER A 71 SHEET 1 AC 3 ARG A 141 ASP A 143 0 SHEET 2 AC 3 PRO A 402 ARG A 404 -1 O ILE A 403 N ALA A 142 SHEET 3 AC 3 ALA A 379 LEU A 380 -1 O ALA A 379 N ARG A 404 SHEET 1 AD 2 VAL A 302 LEU A 304 0 SHEET 2 AD 2 THR A 307 ILE A 309 -1 O THR A 307 N LEU A 304 SHEET 1 BA 4 LEU B 15 ASP B 16 0 SHEET 2 BA 4 ALA B 41 ARG B 45 1 N ARG B 45 O LEU B 15 SHEET 3 BA 4 GLU B 51 VAL B 55 -1 O VAL B 52 N VAL B 44 SHEET 4 BA 4 VAL B 315 VAL B 317 1 O LEU B 316 N VAL B 55 SHEET 1 BB 2 PHE B 70 SER B 71 0 SHEET 2 BB 2 PHE B 297 PRO B 298 -1 O PHE B 297 N SER B 71 SHEET 1 BC 3 ARG B 141 ASP B 143 0 SHEET 2 BC 3 PRO B 402 ARG B 404 -1 O ILE B 403 N ALA B 142 SHEET 3 BC 3 ALA B 379 LEU B 380 -1 O ALA B 379 N ARG B 404 SHEET 1 BD 2 VAL B 302 LEU B 304 0 SHEET 2 BD 2 THR B 307 ILE B 309 -1 O THR B 307 N LEU B 304 LINK SG CYS A 354 FE HEM A1408 1555 1555 2.63 LINK FE HEM A1408 O HOH A2087 1555 1555 2.99 LINK SG CYS B 354 FE HEM B1408 1555 1555 2.68 LINK FE HEM B1408 O HOH B2101 1555 1555 2.88 CISPEP 1 PRO A 97 PRO A 98 0 0.23 CISPEP 2 PRO B 97 PRO B 98 0 0.18 SITE 1 AC1 26 LYS A 72 MET A 92 LEU A 93 HIS A 100 SITE 2 AC1 26 ARG A 104 PHE A 111 ALA A 243 GLY A 244 SITE 3 AC1 26 THR A 247 THR A 248 LEU A 251 PRO A 289 SITE 4 AC1 26 ALA A 293 THR A 294 ARG A 296 ALA A 346 SITE 5 AC1 26 PHE A 347 GLY A 348 ILE A 351 HIS A 352 SITE 6 AC1 26 CYS A 354 ILE A 355 GLY A 356 ALA A 360 SITE 7 AC1 26 HOH A2087 HOH A2144 SITE 1 AC2 5 LEU A 135 ARG A 374 CYS A 375 TRP A 405 SITE 2 AC2 5 HOH A2143 SITE 1 AC3 7 ARG A 120 ASP A 277 ARG A 365 ARG A 369 SITE 2 AC3 7 HOH A2098 GLY B 21 GLN B 22 SITE 1 AC4 24 LYS B 72 MET B 92 LEU B 93 HIS B 100 SITE 2 AC4 24 ARG B 104 PHE B 111 LEU B 240 ALA B 243 SITE 3 AC4 24 GLY B 244 THR B 247 THR B 248 LEU B 251 SITE 4 AC4 24 ALA B 293 THR B 294 ARG B 296 ALA B 346 SITE 5 AC4 24 PHE B 347 GLY B 348 HIS B 352 CYS B 354 SITE 6 AC4 24 ILE B 355 ALA B 360 HOH B2101 HOH B2140 SITE 1 AC5 6 LEU B 135 ARG B 374 CYS B 375 TRP B 405 SITE 2 AC5 6 HOH B2168 HOH B2169 CRYST1 218.190 64.171 73.593 90.00 107.15 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.004583 0.000000 0.001414 0.00000 SCALE2 0.000000 0.015583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014221 0.00000 (ATOM LINES ARE NOT SHOWN.) END
HEADER OXIDOREDUCTASE 09-NOV-05 2C6H TITLE CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 MONOOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYTOCHROME P450 PIKC CYP107L1, CYTOCHROME P450 HYDROXYLASE COMPND 5 PIKC; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE; SOURCE 3 ORGANISM_TAXID: 54571; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS OXIDOREDUCTASE, CYTOCHROME P450, PIKC, CYP107L1, MACROLIDE KEYWDS 2 MONOOXYGENASE, ANTIBIOTIC BIOSYNTHESIS, HEME, IRON, METAL-BINDING, KEYWDS 3 MONOOXYGENASE, OXIDOREDUCTASE ANTIBIOTIC BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR D.H.SHERMAN,S.LI,L.V.YERMALITSKAYA,Y.KIM,J.A.SMITH,M.R.WATERMAN, AUTHOR 2 L.M.PODUST REVDAT 4 13-DEC-23 2C6H 1 LINK REVDAT 3 24-FEB-09 2C6H 1 VERSN REVDAT 2 06-SEP-06 2C6H 1 JRNL REVDAT 1 03-JUL-06 2C6H 0 JRNL AUTH D.H.SHERMAN,S.LI,L.V.YERMALITSKAYA,Y.KIM,J.A.SMITH, JRNL AUTH 2 M.R.WATERMAN,L.M.PODUST JRNL TITL THE STRUCTURAL BASIS FOR SUBSTRATE ANCHORING, ACTIVE SITE JRNL TITL 2 SELECTIVITY, AND PRODUCT FORMATION BY P450 PIKC FROM JRNL TITL 3 STREPTOMYCES VENEZUELAE. JRNL REF J.BIOL.CHEM. V. 281 26289 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16825192 JRNL DOI 10.1074/JBC.M605478200 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 377379.430 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 72999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 7162 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.50 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9489 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 1090 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 175 REMARK 3 SOLVENT ATOMS : 216 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 3.29000 REMARK 3 B33 (A**2) : -3.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.240 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 34.37 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : YC17_NEW.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : YC17_NEW.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISORDERED REGIONS WERE OMMITED FROM REMARK 3 THE STRUCTURE REMARK 4 REMARK 4 2C6H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1290026325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.72196 REMARK 200 MONOCHROMATOR : SI (220) DOUBLE CRYSTAL REMARK 200 OPTICS : SAGITTAL FOCUSING CRYSTAL AND REMARK 200 VERTICALLY FOCUSING DOUBLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41228 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2BVJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG MME 5000, 0.1 M MES, 6.5, 0.5 REMARK 280 MM DTT, 0.2 M AMMONIUM SULFATE, 1 MM YC-17, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.22850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.80950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.80950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.22850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 THR A 4 REMARK 465 GLN A 5 REMARK 465 GLN A 6 REMARK 465 GLY A 7 REMARK 465 THR A 8 REMARK 465 THR A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 PRO A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 408 REMARK 465 ARG A 409 REMARK 465 GLU A 410 REMARK 465 ALA A 411 REMARK 465 GLY A 412 REMARK 465 ARG A 413 REMARK 465 ARG A 414 REMARK 465 THR A 415 REMARK 465 GLY A 416 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 ARG B 3 REMARK 465 THR B 4 REMARK 465 GLN B 5 REMARK 465 GLN B 6 REMARK 465 GLY B 7 REMARK 465 THR B 8 REMARK 465 THR B 9 REMARK 465 ALA B 10 REMARK 465 SER B 11 REMARK 465 PRO B 12 REMARK 465 PRO B 13 REMARK 465 ARG B 409 REMARK 465 GLU B 410 REMARK 465 ALA B 411 REMARK 465 GLY B 412 REMARK 465 ARG B 413 REMARK 465 ARG B 414 REMARK 465 THR B 415 REMARK 465 GLY B 416 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 180 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 406 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 407 CA C O CB CG CD NE REMARK 470 ARG A 407 CZ NH1 NH2 REMARK 470 ARG B 34 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 109 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 407 CG CD NE CZ NH1 NH2 REMARK 470 GLY B 408 CA C O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 148 -57.73 -136.59 REMARK 500 VAL A 179 -70.20 -81.94 REMARK 500 PHE A 180 64.67 -113.80 REMARK 500 HIS A 245 -77.47 -83.12 REMARK 500 ALA A 342 128.12 -38.63 REMARK 500 ALA B 19 -5.20 -57.03 REMARK 500 ASP B 27 79.30 -152.73 REMARK 500 LEU B 148 -51.43 -143.47 REMARK 500 LEU B 228 104.48 -164.44 REMARK 500 HIS B 245 -72.90 -77.19 REMARK 500 CYS B 354 116.04 -36.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1407 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 354 SG REMARK 620 2 HEM A1407 NA 98.9 REMARK 620 3 HEM A1407 NB 87.6 90.0 REMARK 620 4 HEM A1407 NC 87.6 173.4 89.1 REMARK 620 5 HEM A1407 ND 101.9 90.0 170.4 89.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B1408 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 354 SG REMARK 620 2 HEM B1408 NA 96.7 REMARK 620 3 HEM B1408 NB 92.3 89.4 REMARK 620 4 HEM B1408 NC 89.6 173.6 89.0 REMARK 620 5 HEM B1408 ND 100.6 88.7 167.1 91.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1431 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1432 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1434 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXI A1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXI B1409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BVJ RELATED DB: PDB REMARK 900 LIGAND-FREE STRUCTURE OF CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2C7X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NARBOMYCIN-BOUND CYTOCHROME P450 PIKC REMARK 900 (CYP107L1) REMARK 900 RELATED ID: 2CA0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2CD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN REMARK 999 CLEAVAGE SITE ARE FROM THE CLONING VECTOR PET28A DBREF 2C6H A -19 0 PDB 2C6H 2C6H -19 0 DBREF 2C6H A 1 416 UNP O87605 O87605_9ACTO 1 416 DBREF 2C6H B -19 0 PDB 2C6H 2C6H -19 0 DBREF 2C6H B 1 416 UNP O87605 O87605_9ACTO 1 416 SEQRES 1 A 436 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 436 LEU VAL PRO ARG GLY SER HIS MET ARG ARG THR GLN GLN SEQRES 3 A 436 GLY THR THR ALA SER PRO PRO VAL LEU ASP LEU GLY ALA SEQRES 4 A 436 LEU GLY GLN ASP PHE ALA ALA ASP PRO TYR PRO THR TYR SEQRES 5 A 436 ALA ARG LEU ARG ALA GLU GLY PRO ALA HIS ARG VAL ARG SEQRES 6 A 436 THR PRO GLU GLY ASP GLU VAL TRP LEU VAL VAL GLY TYR SEQRES 7 A 436 ASP ARG ALA ARG ALA VAL LEU ALA ASP PRO ARG PHE SER SEQRES 8 A 436 LYS ASP TRP ARG ASN SER THR THR PRO LEU THR GLU ALA SEQRES 9 A 436 GLU ALA ALA LEU ASN HIS ASN MET LEU GLU SER ASP PRO SEQRES 10 A 436 PRO ARG HIS THR ARG LEU ARG LYS LEU VAL ALA ARG GLU SEQRES 11 A 436 PHE THR MET ARG ARG VAL GLU LEU LEU ARG PRO ARG VAL SEQRES 12 A 436 GLN GLU ILE VAL ASP GLY LEU VAL ASP ALA MET LEU ALA SEQRES 13 A 436 ALA PRO ASP GLY ARG ALA ASP LEU MET GLU SER LEU ALA SEQRES 14 A 436 TRP PRO LEU PRO ILE THR VAL ILE SER GLU LEU LEU GLY SEQRES 15 A 436 VAL PRO GLU PRO ASP ARG ALA ALA PHE ARG VAL TRP THR SEQRES 16 A 436 ASP ALA PHE VAL PHE PRO ASP ASP PRO ALA GLN ALA GLN SEQRES 17 A 436 THR ALA MET ALA GLU MET SER GLY TYR LEU SER ARG LEU SEQRES 18 A 436 ILE ASP SER LYS ARG GLY GLN ASP GLY GLU ASP LEU LEU SEQRES 19 A 436 SER ALA LEU VAL ARG THR SER ASP GLU ASP GLY SER ARG SEQRES 20 A 436 LEU THR SER GLU GLU LEU LEU GLY MET ALA HIS ILE LEU SEQRES 21 A 436 LEU VAL ALA GLY HIS GLU THR THR VAL ASN LEU ILE ALA SEQRES 22 A 436 ASN GLY MET TYR ALA LEU LEU SER HIS PRO ASP GLN LEU SEQRES 23 A 436 ALA ALA LEU ARG ALA ASP MET THR LEU LEU ASP GLY ALA SEQRES 24 A 436 VAL GLU GLU MET LEU ARG TYR GLU GLY PRO VAL GLU SER SEQRES 25 A 436 ALA THR TYR ARG PHE PRO VAL GLU PRO VAL ASP LEU ASP SEQRES 26 A 436 GLY THR VAL ILE PRO ALA GLY ASP THR VAL LEU VAL VAL SEQRES 27 A 436 LEU ALA ASP ALA HIS ARG THR PRO GLU ARG PHE PRO ASP SEQRES 28 A 436 PRO HIS ARG PHE ASP ILE ARG ARG ASP THR ALA GLY HIS SEQRES 29 A 436 LEU ALA PHE GLY HIS GLY ILE HIS PHE CYS ILE GLY ALA SEQRES 30 A 436 PRO LEU ALA ARG LEU GLU ALA ARG ILE ALA VAL ARG ALA SEQRES 31 A 436 LEU LEU GLU ARG CYS PRO ASP LEU ALA LEU ASP VAL SER SEQRES 32 A 436 PRO GLY GLU LEU VAL TRP TYR PRO ASN PRO MET ILE ARG SEQRES 33 A 436 GLY LEU LYS ALA LEU PRO ILE ARG TRP ARG ARG GLY ARG SEQRES 34 A 436 GLU ALA GLY ARG ARG THR GLY SEQRES 1 B 436 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 436 LEU VAL PRO ARG GLY SER HIS MET ARG ARG THR GLN GLN SEQRES 3 B 436 GLY THR THR ALA SER PRO PRO VAL LEU ASP LEU GLY ALA SEQRES 4 B 436 LEU GLY GLN ASP PHE ALA ALA ASP PRO TYR PRO THR TYR SEQRES 5 B 436 ALA ARG LEU ARG ALA GLU GLY PRO ALA HIS ARG VAL ARG SEQRES 6 B 436 THR PRO GLU GLY ASP GLU VAL TRP LEU VAL VAL GLY TYR SEQRES 7 B 436 ASP ARG ALA ARG ALA VAL LEU ALA ASP PRO ARG PHE SER SEQRES 8 B 436 LYS ASP TRP ARG ASN SER THR THR PRO LEU THR GLU ALA SEQRES 9 B 436 GLU ALA ALA LEU ASN HIS ASN MET LEU GLU SER ASP PRO SEQRES 10 B 436 PRO ARG HIS THR ARG LEU ARG LYS LEU VAL ALA ARG GLU SEQRES 11 B 436 PHE THR MET ARG ARG VAL GLU LEU LEU ARG PRO ARG VAL SEQRES 12 B 436 GLN GLU ILE VAL ASP GLY LEU VAL ASP ALA MET LEU ALA SEQRES 13 B 436 ALA PRO ASP GLY ARG ALA ASP LEU MET GLU SER LEU ALA SEQRES 14 B 436 TRP PRO LEU PRO ILE THR VAL ILE SER GLU LEU LEU GLY SEQRES 15 B 436 VAL PRO GLU PRO ASP ARG ALA ALA PHE ARG VAL TRP THR SEQRES 16 B 436 ASP ALA PHE VAL PHE PRO ASP ASP PRO ALA GLN ALA GLN SEQRES 17 B 436 THR ALA MET ALA GLU MET SER GLY TYR LEU SER ARG LEU SEQRES 18 B 436 ILE ASP SER LYS ARG GLY GLN ASP GLY GLU ASP LEU LEU SEQRES 19 B 436 SER ALA LEU VAL ARG THR SER ASP GLU ASP GLY SER ARG SEQRES 20 B 436 LEU THR SER GLU GLU LEU LEU GLY MET ALA HIS ILE LEU SEQRES 21 B 436 LEU VAL ALA GLY HIS GLU THR THR VAL ASN LEU ILE ALA SEQRES 22 B 436 ASN GLY MET TYR ALA LEU LEU SER HIS PRO ASP GLN LEU SEQRES 23 B 436 ALA ALA LEU ARG ALA ASP MET THR LEU LEU ASP GLY ALA SEQRES 24 B 436 VAL GLU GLU MET LEU ARG TYR GLU GLY PRO VAL GLU SER SEQRES 25 B 436 ALA THR TYR ARG PHE PRO VAL GLU PRO VAL ASP LEU ASP SEQRES 26 B 436 GLY THR VAL ILE PRO ALA GLY ASP THR VAL LEU VAL VAL SEQRES 27 B 436 LEU ALA ASP ALA HIS ARG THR PRO GLU ARG PHE PRO ASP SEQRES 28 B 436 PRO HIS ARG PHE ASP ILE ARG ARG ASP THR ALA GLY HIS SEQRES 29 B 436 LEU ALA PHE GLY HIS GLY ILE HIS PHE CYS ILE GLY ALA SEQRES 30 B 436 PRO LEU ALA ARG LEU GLU ALA ARG ILE ALA VAL ARG ALA SEQRES 31 B 436 LEU LEU GLU ARG CYS PRO ASP LEU ALA LEU ASP VAL SER SEQRES 32 B 436 PRO GLY GLU LEU VAL TRP TYR PRO ASN PRO MET ILE ARG SEQRES 33 B 436 GLY LEU LYS ALA LEU PRO ILE ARG TRP ARG ARG GLY ARG SEQRES 34 B 436 GLU ALA GLY ARG ARG THR GLY HET HEM A1407 43 HET PXI A1408 32 HET SO4 A1430 5 HET SO4 A1431 5 HET SO4 A1432 5 HET SO4 A1434 5 HET HEM B1408 43 HET PXI B1409 32 HET SO4 B1433 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PXI 4-{[4-(DIMETHYLAMINO)-3-HYDROXY-6-METHYLTETRAHYDRO-2H- HETNAM 2 PXI PYRAN-2-YL]OXY}-12-ETHYL-3,5,7,11- HETNAM 3 PXI TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 PXI 2(C25 H43 N O6) FORMUL 5 SO4 5(O4 S 2-) FORMUL 12 HOH *216(H2 O) HELIX 1 1 LEU A 20 ASP A 27 1 8 HELIX 2 2 PRO A 28 GLY A 39 1 12 HELIX 3 3 GLY A 57 ASP A 67 1 11 HELIX 4 4 ASP A 73 SER A 77 5 5 HELIX 5 5 ASN A 91 SER A 95 5 5 HELIX 6 6 PRO A 98 LEU A 106 1 9 HELIX 7 7 VAL A 107 PHE A 111 5 5 HELIX 8 8 THR A 112 LEU A 118 1 7 HELIX 9 9 LEU A 119 LEU A 135 1 17 HELIX 10 10 LEU A 144 LEU A 148 1 5 HELIX 11 11 TRP A 150 GLY A 162 1 13 HELIX 12 12 PRO A 164 PRO A 166 5 3 HELIX 13 13 ASP A 167 PHE A 180 1 14 HELIX 14 14 ASP A 183 ARG A 206 1 24 HELIX 15 15 ASP A 212 ASP A 224 1 13 HELIX 16 16 THR A 229 ALA A 243 1 15 HELIX 17 17 GLY A 244 SER A 261 1 18 HELIX 18 18 HIS A 262 ASP A 272 1 11 HELIX 19 19 LEU A 275 GLY A 288 1 14 HELIX 20 20 VAL A 318 HIS A 323 1 6 HELIX 21 21 GLY A 356 CYS A 375 1 20 HELIX 22 22 SER A 383 LEU A 387 5 5 HELIX 23 23 LEU B 20 ASP B 27 1 8 HELIX 24 24 PRO B 28 ALA B 37 1 10 HELIX 25 25 GLY B 57 ASP B 67 1 11 HELIX 26 26 ASP B 73 SER B 77 5 5 HELIX 27 27 ALA B 84 LEU B 88 5 5 HELIX 28 28 ASN B 91 SER B 95 5 5 HELIX 29 29 PRO B 98 LEU B 106 1 9 HELIX 30 30 VAL B 107 PHE B 111 5 5 HELIX 31 31 THR B 112 GLU B 117 1 6 HELIX 32 32 LEU B 119 LEU B 135 1 17 HELIX 33 33 LEU B 144 LEU B 148 1 5 HELIX 34 34 TRP B 150 GLY B 162 1 13 HELIX 35 35 PRO B 164 PHE B 180 1 17 HELIX 36 36 ASP B 183 ARG B 206 1 24 HELIX 37 37 ASP B 212 ASP B 224 1 13 HELIX 38 38 THR B 229 ALA B 243 1 15 HELIX 39 39 GLY B 244 SER B 261 1 18 HELIX 40 40 HIS B 262 ASP B 272 1 11 HELIX 41 41 LEU B 275 GLY B 288 1 14 HELIX 42 42 VAL B 318 HIS B 323 1 6 HELIX 43 43 GLY B 356 CYS B 375 1 20 HELIX 44 44 SER B 383 LEU B 387 5 5 SHEET 1 AA 4 LEU A 15 ASP A 16 0 SHEET 2 AA 4 ALA A 41 ARG A 45 1 O ARG A 43 N LEU A 15 SHEET 3 AA 4 GLU A 51 VAL A 55 -1 O VAL A 52 N VAL A 44 SHEET 4 AA 4 VAL A 315 VAL A 317 1 O LEU A 316 N VAL A 55 SHEET 1 AB 2 PHE A 70 SER A 71 0 SHEET 2 AB 2 PHE A 297 PRO A 298 -1 O PHE A 297 N SER A 71 SHEET 1 AC 3 ARG A 141 ASP A 143 0 SHEET 2 AC 3 PRO A 402 ARG A 404 -1 O ILE A 403 N ALA A 142 SHEET 3 AC 3 ALA A 379 LEU A 380 -1 O ALA A 379 N ARG A 404 SHEET 1 AD 2 VAL A 302 LEU A 304 0 SHEET 2 AD 2 THR A 307 ILE A 309 -1 O THR A 307 N LEU A 304 SHEET 1 BA 4 LEU B 15 ASP B 16 0 SHEET 2 BA 4 ALA B 41 ARG B 45 1 O ARG B 43 N LEU B 15 SHEET 3 BA 4 GLU B 51 VAL B 55 -1 O VAL B 52 N VAL B 44 SHEET 4 BA 4 VAL B 315 VAL B 317 1 O LEU B 316 N VAL B 55 SHEET 1 BB 2 PHE B 70 SER B 71 0 SHEET 2 BB 2 PHE B 297 PRO B 298 -1 O PHE B 297 N SER B 71 SHEET 1 BC 3 ARG B 141 ASP B 143 0 SHEET 2 BC 3 PRO B 402 ARG B 404 -1 O ILE B 403 N ALA B 142 SHEET 3 BC 3 ALA B 379 LEU B 380 -1 O ALA B 379 N ARG B 404 SHEET 1 BD 2 VAL B 302 LEU B 304 0 SHEET 2 BD 2 THR B 307 ILE B 309 -1 O THR B 307 N LEU B 304 LINK SG CYS A 354 FE HEM A1407 1555 1555 2.42 LINK SG CYS B 354 FE HEM B1408 1555 1555 2.45 CISPEP 1 PRO A 97 PRO A 98 0 0.18 CISPEP 2 PRO B 97 PRO B 98 0 0.28 SITE 1 AC1 3 ARG A 62 THR A 220 ARG A 227 SITE 1 AC2 3 ARG A 99 ARG A 102 HOH A2027 SITE 1 AC3 6 GLU A 223 ASP A 224 GLY A 343 HIS A 344 SITE 2 AC3 6 HOH A2088 HOH A2107 SITE 1 AC4 6 ARG A 75 HIS A 90 ARG A 99 HOH A2108 SITE 2 AC4 6 HOH A2109 THR B 78 SITE 1 AC5 3 ARG B 62 THR B 220 ARG B 227 SITE 1 AC6 26 LYS A 72 MET A 92 LEU A 93 HIS A 100 SITE 2 AC6 26 ARG A 104 PHE A 111 ILE A 157 LEU A 240 SITE 3 AC6 26 ALA A 243 GLY A 244 THR A 247 THR A 248 SITE 4 AC6 26 LEU A 251 PRO A 289 ALA A 293 THR A 294 SITE 5 AC6 26 ARG A 296 ALA A 346 PHE A 347 GLY A 348 SITE 6 AC6 26 ILE A 351 HIS A 352 CYS A 354 ILE A 355 SITE 7 AC6 26 PXI A1408 HOH A2105 SITE 1 AC7 14 LEU A 81 GLU A 85 LEU A 93 GLU A 94 SITE 2 AC7 14 PHE A 178 VAL A 179 HIS A 238 VAL A 242 SITE 3 AC7 14 ALA A 243 GLU A 246 THR A 247 VAL A 290 SITE 4 AC7 14 ILE A 395 HEM A1407 SITE 1 AC8 24 MET B 92 LEU B 93 HIS B 100 ARG B 104 SITE 2 AC8 24 PHE B 111 LEU B 240 ALA B 243 GLY B 244 SITE 3 AC8 24 THR B 247 THR B 248 LEU B 251 PRO B 289 SITE 4 AC8 24 ALA B 293 THR B 294 ARG B 296 ALA B 346 SITE 5 AC8 24 PHE B 347 GLY B 348 ILE B 351 HIS B 352 SITE 6 AC8 24 CYS B 354 ILE B 355 ALA B 360 HOH B2096 SITE 1 AC9 16 LEU B 81 GLU B 85 LEU B 88 ASN B 89 SITE 2 AC9 16 LEU B 93 GLU B 94 VAL B 179 HIS B 238 SITE 3 AC9 16 VAL B 242 ALA B 243 GLU B 246 VAL B 290 SITE 4 AC9 16 THR B 294 MET B 394 HOH B2106 HOH B2107 CRYST1 60.457 104.700 153.619 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016541 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009551 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006510 0.00000 MTRIX1 1 0.999830 0.018200 0.001490 -42.15639 1 MTRIX2 1 -0.017800 0.989680 -0.142190 -41.77388 1 MTRIX3 1 -0.004060 0.142140 0.989840 -3.07427 1 (ATOM LINES ARE NOT SHOWN.) END
HEADER OXIDOREDUCTASE 29-NOV-05 2C7X TITLE CRYSTAL STRUCTURE OF NARBOMYCIN-BOUND CYTOCHROME P450 PIKC (CYP107L1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 MONOOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME P450 PIKC CYP107L1, CYTOCHROME P450 HYDROXYLASE COMPND 5 PIKC; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE; SOURCE 3 ORGANISM_TAXID: 54571; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CYTOCHROME P450, PIKC, NARBOMYCIN, MACROLIDE MONOOXYGENASE, KEYWDS 2 ANTIBIOTIC BIOSYNTHESIS, HEME, IRON, METAL-BINDING, MONOOXYGENASE, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.H.SHERMAN,S.LI,L.V.YERMALITSKAYA,Y.KIM,J.A.SMITH,M.R.WATERMAN, AUTHOR 2 L.M.PODUST REVDAT 5 13-DEC-23 2C7X 1 LINK REVDAT 4 08-MAY-19 2C7X 1 REMARK REVDAT 3 24-FEB-09 2C7X 1 VERSN REVDAT 2 06-SEP-06 2C7X 1 JRNL REVDAT 1 03-JUL-06 2C7X 0 JRNL AUTH D.H.SHERMAN,S.LI,L.V.YERMALITSKAYA,Y.KIM,J.A.SMITH, JRNL AUTH 2 M.R.WATERMAN,L.M.PODUST JRNL TITL THE STRUCTURAL BASIS FOR SUBSTRATE ANCHORING, ACTIVE SITE JRNL TITL 2 SELECTIVITY, AND PRODUCT FORMATION BY P450 PIKC FROM JRNL TITL 3 STREPTOMYCES VENEZUELAE. JRNL REF J.BIOL.CHEM. V. 281 26289 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16825192 JRNL DOI 10.1074/JBC.M605478200 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 329931.620 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 34218 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3408 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3940 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 420 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 7.41000 REMARK 3 B33 (A**2) : -7.78000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.400 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.140 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.280 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 52.10 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISORDERED REGIONS WERE OMMITED FROM REMARK 3 THE STRUCTURE REMARK 4 REMARK 4 2C7X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1290026596. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97952 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : SAGITTAL FOCUSING CRYSTAL AND REMARK 200 VERTICAL FOCUSING DOUBLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36334 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 65.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2BVJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 6.0 0.8 M AMMONIUM SULFATE, REMARK 280 0.5 MM DTT, 1 MM NARBOMYCIN, T=20 C, PH 6.00, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.48150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.41500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.44800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.41500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.48150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.44800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 THR A 4 REMARK 465 GLN A 5 REMARK 465 GLN A 6 REMARK 465 GLY A 7 REMARK 465 THR A 8 REMARK 465 THR A 9 REMARK 465 ALA A 10 REMARK 465 GLY A 408 REMARK 465 ARG A 409 REMARK 465 GLU A 410 REMARK 465 ALA A 411 REMARK 465 GLY A 412 REMARK 465 ARG A 413 REMARK 465 ARG A 414 REMARK 465 THR A 415 REMARK 465 GLY A 416 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 11 OG REMARK 470 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 182 CG OD1 OD2 REMARK 470 ASP A 183 CG OD1 OD2 REMARK 470 GLU A 300 CG CD OE1 OE2 REMARK 470 SER A 383 OG REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 ARG A 406 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 407 CA C O CB CG CD NE REMARK 470 ARG A 407 CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CG2 THR A 175 OE1 GLU A 246 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 13 CD PRO A 13 N -0.356 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 13 N - CD - CG ANGL. DEV. = 12.5 DEGREES REMARK 500 PRO A 184 C - N - CD ANGL. DEV. = -14.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 148 -49.70 -142.99 REMARK 500 PRO A 181 -137.80 -49.58 REMARK 500 ASP A 182 1.14 -179.81 REMARK 500 ASP A 183 151.12 169.39 REMARK 500 HIS A 245 -76.86 -73.09 REMARK 500 ASP A 381 54.02 -113.11 REMARK 500 VAL A 382 143.59 174.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1407 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 354 SG REMARK 620 2 HEM A1407 NA 98.1 REMARK 620 3 HEM A1407 NB 88.4 90.0 REMARK 620 4 HEM A1407 NC 86.7 175.1 90.7 REMARK 620 5 HEM A1407 ND 103.1 89.3 168.5 89.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NRB A1408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BVJ RELATED DB: PDB REMARK 900 LIGAND-FREE STRUCTURE OF CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2C6H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2CA0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2CD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN REMARK 999 CLEAVAGE SITE ARE FROM THE CLONING VECTOR PET28A DBREF 2C7X A -19 0 PDB 2C7X 2C7X -19 0 DBREF 2C7X A 1 416 UNP O87605 O87605_9ACTO 1 416 SEQRES 1 A 436 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 436 LEU VAL PRO ARG GLY SER HIS MET ARG ARG THR GLN GLN SEQRES 3 A 436 GLY THR THR ALA SER PRO PRO VAL LEU ASP LEU GLY ALA SEQRES 4 A 436 LEU GLY GLN ASP PHE ALA ALA ASP PRO TYR PRO THR TYR SEQRES 5 A 436 ALA ARG LEU ARG ALA GLU GLY PRO ALA HIS ARG VAL ARG SEQRES 6 A 436 THR PRO GLU GLY ASP GLU VAL TRP LEU VAL VAL GLY TYR SEQRES 7 A 436 ASP ARG ALA ARG ALA VAL LEU ALA ASP PRO ARG PHE SER SEQRES 8 A 436 LYS ASP TRP ARG ASN SER THR THR PRO LEU THR GLU ALA SEQRES 9 A 436 GLU ALA ALA LEU ASN HIS ASN MET LEU GLU SER ASP PRO SEQRES 10 A 436 PRO ARG HIS THR ARG LEU ARG LYS LEU VAL ALA ARG GLU SEQRES 11 A 436 PHE THR MET ARG ARG VAL GLU LEU LEU ARG PRO ARG VAL SEQRES 12 A 436 GLN GLU ILE VAL ASP GLY LEU VAL ASP ALA MET LEU ALA SEQRES 13 A 436 ALA PRO ASP GLY ARG ALA ASP LEU MET GLU SER LEU ALA SEQRES 14 A 436 TRP PRO LEU PRO ILE THR VAL ILE SER GLU LEU LEU GLY SEQRES 15 A 436 VAL PRO GLU PRO ASP ARG ALA ALA PHE ARG VAL TRP THR SEQRES 16 A 436 ASP ALA PHE VAL PHE PRO ASP ASP PRO ALA GLN ALA GLN SEQRES 17 A 436 THR ALA MET ALA GLU MET SER GLY TYR LEU SER ARG LEU SEQRES 18 A 436 ILE ASP SER LYS ARG GLY GLN ASP GLY GLU ASP LEU LEU SEQRES 19 A 436 SER ALA LEU VAL ARG THR SER ASP GLU ASP GLY SER ARG SEQRES 20 A 436 LEU THR SER GLU GLU LEU LEU GLY MET ALA HIS ILE LEU SEQRES 21 A 436 LEU VAL ALA GLY HIS GLU THR THR VAL ASN LEU ILE ALA SEQRES 22 A 436 ASN GLY MET TYR ALA LEU LEU SER HIS PRO ASP GLN LEU SEQRES 23 A 436 ALA ALA LEU ARG ALA ASP MET THR LEU LEU ASP GLY ALA SEQRES 24 A 436 VAL GLU GLU MET LEU ARG TYR GLU GLY PRO VAL GLU SER SEQRES 25 A 436 ALA THR TYR ARG PHE PRO VAL GLU PRO VAL ASP LEU ASP SEQRES 26 A 436 GLY THR VAL ILE PRO ALA GLY ASP THR VAL LEU VAL VAL SEQRES 27 A 436 LEU ALA ASP ALA HIS ARG THR PRO GLU ARG PHE PRO ASP SEQRES 28 A 436 PRO HIS ARG PHE ASP ILE ARG ARG ASP THR ALA GLY HIS SEQRES 29 A 436 LEU ALA PHE GLY HIS GLY ILE HIS PHE CYS ILE GLY ALA SEQRES 30 A 436 PRO LEU ALA ARG LEU GLU ALA ARG ILE ALA VAL ARG ALA SEQRES 31 A 436 LEU LEU GLU ARG CYS PRO ASP LEU ALA LEU ASP VAL SER SEQRES 32 A 436 PRO GLY GLU LEU VAL TRP TYR PRO ASN PRO MET ILE ARG SEQRES 33 A 436 GLY LEU LYS ALA LEU PRO ILE ARG TRP ARG ARG GLY ARG SEQRES 34 A 436 GLU ALA GLY ARG ARG THR GLY HET HEM A1407 43 HET NRB A1408 36 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NRB NARBOMYCIN HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 NRB C28 H47 N O7 FORMUL 4 HOH *166(H2 O) HELIX 1 1 GLY A 21 ASP A 27 1 7 HELIX 2 2 PRO A 28 GLY A 39 1 12 HELIX 3 3 GLY A 57 ASP A 67 1 11 HELIX 4 4 ASP A 73 SER A 77 5 5 HELIX 5 5 THR A 82 ASN A 89 1 8 HELIX 6 6 ASN A 91 SER A 95 5 5 HELIX 7 7 PRO A 98 LEU A 106 1 9 HELIX 8 8 VAL A 107 PHE A 111 5 5 HELIX 9 9 THR A 112 LEU A 118 1 7 HELIX 10 10 LEU A 119 LEU A 135 1 17 HELIX 11 11 LEU A 144 LEU A 148 1 5 HELIX 12 12 TRP A 150 GLY A 162 1 13 HELIX 13 13 PRO A 164 ASP A 167 5 4 HELIX 14 14 ARG A 168 PHE A 180 1 13 HELIX 15 15 ASP A 183 ARG A 206 1 24 HELIX 16 16 ASP A 212 ASP A 224 1 13 HELIX 17 17 THR A 229 SER A 261 1 33 HELIX 18 18 HIS A 262 ASP A 272 1 11 HELIX 19 19 LEU A 275 GLY A 288 1 14 HELIX 20 20 VAL A 318 HIS A 323 1 6 HELIX 21 21 GLY A 356 CYS A 375 1 20 HELIX 22 22 SER A 383 LEU A 387 5 5 SHEET 1 AA 4 LEU A 15 ASP A 16 0 SHEET 2 AA 4 ALA A 41 ARG A 45 1 N ARG A 45 O LEU A 15 SHEET 3 AA 4 GLU A 51 VAL A 55 -1 O VAL A 52 N VAL A 44 SHEET 4 AA 4 VAL A 315 VAL A 317 1 O LEU A 316 N VAL A 55 SHEET 1 AB 2 PHE A 70 SER A 71 0 SHEET 2 AB 2 PHE A 297 PRO A 298 -1 O PHE A 297 N SER A 71 SHEET 1 AC 3 ARG A 141 ASP A 143 0 SHEET 2 AC 3 PRO A 402 ARG A 404 -1 O ILE A 403 N ALA A 142 SHEET 3 AC 3 ALA A 379 LEU A 380 -1 O ALA A 379 N ARG A 404 SHEET 1 AD 2 VAL A 302 LEU A 304 0 SHEET 2 AD 2 THR A 307 ILE A 309 -1 O THR A 307 N LEU A 304 LINK SG CYS A 354 FE HEM A1407 1555 1555 2.66 CISPEP 1 PRO A 97 PRO A 98 0 0.20 SITE 1 AC1 26 LYS A 72 MET A 92 LEU A 93 HIS A 100 SITE 2 AC1 26 ARG A 104 PHE A 111 ALA A 243 GLY A 244 SITE 3 AC1 26 THR A 247 THR A 248 LEU A 251 PRO A 289 SITE 4 AC1 26 ALA A 293 THR A 294 ARG A 296 ALA A 346 SITE 5 AC1 26 PHE A 347 GLY A 348 ILE A 351 HIS A 352 SITE 6 AC1 26 CYS A 354 ILE A 355 GLY A 356 ALA A 360 SITE 7 AC1 26 NRB A1408 HOH A2166 SITE 1 AC2 15 ASP A 50 GLU A 85 PHE A 178 MET A 191 SITE 2 AC2 15 HIS A 238 ILE A 239 VAL A 242 ALA A 243 SITE 3 AC2 15 GLU A 246 THR A 294 ASN A 392 MET A 394 SITE 4 AC2 15 ILE A 395 HEM A1407 HOH A2048 CRYST1 58.963 64.896 92.830 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010772 0.00000 (ATOM LINES ARE NOT SHOWN.) END
HEADER OXIDOREDUCTASE 20-JAN-06 2CD8 TITLE CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 MONOOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYTOCHROME P450 HYDROXYLASE PIKC, CYTOCHROME P450 PIKC COMPND 5 CYP107L1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE; SOURCE 3 ORGANISM_TAXID: 54571; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS OXIDOREDUCTASE, CYTOCHROME P450, PIKC, YC-17, MACROLIDE KEYWDS 2 MONOOXYGENASE, ANTIBIOTIC BIOSYNTHESIS, HEME, IRON, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.I.YERMALITSKAYA,Y.KIM,D.H.SHERMAN,M.R.WATERMAN,L.M.PODUST REVDAT 3 13-DEC-23 2CD8 1 REMARK LINK REVDAT 2 24-FEB-09 2CD8 1 VERSN REVDAT 1 20-FEB-07 2CD8 0 JRNL AUTH D.H.SHERMAN,S.LI,L.V.YERMALITSKAYA,Y.KIM,J.A.SMITH, JRNL AUTH 2 M.R.WATERMAN,L.M.PODUST JRNL TITL THE STRUCTURAL BASIS FOR SUBSTRATE ANCHORING, ACTIVE SITE JRNL TITL 2 SELECTIVITY, AND PRODUCT FORMATION BY P450 PIKC FROM JRNL TITL 3 STREPTOMYCES VENEZUELAE. JRNL REF J.BIOL.CHEM. V. 281 26289 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16825192 JRNL DOI 10.1074/JBC.M605478200 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 153672.180 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 71229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.290 REMARK 3 FREE R VALUE : 0.333 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7136 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8371 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 913 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 150 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -4.13000 REMARK 3 B33 (A**2) : 4.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.100 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.920 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.350 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 66.42 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISORDERED REGIONS WERE OMITTED FROM REMARK 3 THE STRUCTURE REMARK 4 REMARK 4 2CD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1290027375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2BVJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M MGCL2, 0.5 MM DTT, REMARK 280 1 MM YC-17, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 46.05100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 THR A 4 REMARK 465 GLN A 5 REMARK 465 GLN A 6 REMARK 465 GLY A 7 REMARK 465 THR A 8 REMARK 465 THR A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 PRO A 12 REMARK 465 PRO A 13 REMARK 465 ARG A 406 REMARK 465 ARG A 407 REMARK 465 GLY A 408 REMARK 465 ARG A 409 REMARK 465 GLU A 410 REMARK 465 ALA A 411 REMARK 465 GLY A 412 REMARK 465 ARG A 413 REMARK 465 ARG A 414 REMARK 465 THR A 415 REMARK 465 GLY A 416 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 ARG B 3 REMARK 465 THR B 4 REMARK 465 GLN B 5 REMARK 465 GLN B 6 REMARK 465 GLY B 7 REMARK 465 THR B 8 REMARK 465 THR B 9 REMARK 465 ALA B 10 REMARK 465 SER B 11 REMARK 465 PRO B 12 REMARK 465 PRO B 13 REMARK 465 ARG B 407 REMARK 465 GLY B 408 REMARK 465 ARG B 409 REMARK 465 GLU B 410 REMARK 465 ALA B 411 REMARK 465 GLY B 412 REMARK 465 ARG B 413 REMARK 465 ARG B 414 REMARK 465 THR B 415 REMARK 465 GLY B 416 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 180 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 300 CG CD OE1 OE2 REMARK 470 TRP A 405 CA C O CB CG CD1 CD2 REMARK 470 TRP A 405 NE1 CE2 CE3 CZ2 CZ3 CH2 REMARK 470 GLU B 51 CG CD OE1 OE2 REMARK 470 GLU B 83 CG CD OE1 OE2 REMARK 470 ARG B 109 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 180 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 300 CG CD OE1 OE2 REMARK 470 ASP B 377 CG OD1 OD2 REMARK 470 ARG B 406 CA C O CB CG CD NE REMARK 470 ARG B 406 CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 38 -63.30 -92.99 REMARK 500 TYR A 58 -70.72 -32.93 REMARK 500 GLU A 94 52.87 -111.72 REMARK 500 ALA A 137 105.48 -51.80 REMARK 500 PRO A 138 25.60 -67.24 REMARK 500 LEU A 148 -53.95 -139.08 REMARK 500 ASP A 183 152.15 172.43 REMARK 500 PRO A 184 3.25 -57.89 REMARK 500 HIS A 245 -83.51 -76.09 REMARK 500 GLU A 287 52.12 -149.22 REMARK 500 ALA A 342 124.12 -28.83 REMARK 500 CYS A 354 115.00 -37.60 REMARK 500 ARG A 374 -81.36 -55.74 REMARK 500 CYS A 375 92.73 -35.57 REMARK 500 ASP A 377 52.03 -99.93 REMARK 500 ASP A 381 42.82 -106.46 REMARK 500 GLU B 117 1.60 -69.09 REMARK 500 LEU B 135 42.69 -74.91 REMARK 500 LEU B 148 -60.19 -145.00 REMARK 500 LEU B 160 36.53 -86.53 REMARK 500 LEU B 161 -37.58 -159.35 REMARK 500 ASP B 182 -8.71 -58.95 REMARK 500 ASP B 183 145.74 -178.70 REMARK 500 ASP B 224 107.66 -163.10 REMARK 500 SER B 226 -48.61 -134.62 REMARK 500 LEU B 228 108.96 -160.68 REMARK 500 HIS B 245 -78.36 -93.26 REMARK 500 ASP B 272 49.17 -147.35 REMARK 500 MET B 273 -12.65 -47.62 REMARK 500 LEU B 276 -72.79 -42.52 REMARK 500 ASP B 305 -8.07 59.86 REMARK 500 ALA B 342 75.07 -66.44 REMARK 500 HIS B 349 142.10 -171.17 REMARK 500 CYS B 354 113.88 -39.06 REMARK 500 ASP B 381 35.81 -96.34 REMARK 500 VAL B 382 -171.93 -178.08 REMARK 500 ASN B 392 122.30 -26.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 419 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 354 SG REMARK 620 2 HEM A 419 NA 97.7 REMARK 620 3 HEM A 419 NB 86.8 91.3 REMARK 620 4 HEM A 419 NC 87.3 174.6 90.9 REMARK 620 5 HEM A 419 ND 102.8 88.4 170.3 88.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 419 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 354 SG REMARK 620 2 HEM B 419 NA 99.2 REMARK 620 3 HEM B 419 NB 81.0 90.5 REMARK 620 4 HEM B 419 NC 85.5 175.3 89.5 REMARK 620 5 HEM B 419 ND 109.7 90.1 169.1 89.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXI A 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXI B 420 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BVJ RELATED DB: PDB REMARK 900 LIGAND-FREE STRUCTURE OF CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2C6H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 900 RELATED ID: 2C7X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NARBOMYCIN-BOUND CYTOCHROME P450 PIKC REMARK 900 (CYP107L1) REMARK 900 RELATED ID: 2CA0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1) REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN REMARK 999 CLEAVAGE SITE ARE FROM THE CLONING VECTOR PET28A DBREF 2CD8 A -19 0 PDB 2CD8 2CD8 -19 0 DBREF 2CD8 A 1 416 UNP O87605 O87605_9ACTO 1 416 DBREF 2CD8 B -19 0 PDB 2CD8 2CD8 -19 0 DBREF 2CD8 B 1 416 UNP O87605 O87605_9ACTO 1 416 SEQRES 1 A 436 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 436 LEU VAL PRO ARG GLY SER HIS MET ARG ARG THR GLN GLN SEQRES 3 A 436 GLY THR THR ALA SER PRO PRO VAL LEU ASP LEU GLY ALA SEQRES 4 A 436 LEU GLY GLN ASP PHE ALA ALA ASP PRO TYR PRO THR TYR SEQRES 5 A 436 ALA ARG LEU ARG ALA GLU GLY PRO ALA HIS ARG VAL ARG SEQRES 6 A 436 THR PRO GLU GLY ASP GLU VAL TRP LEU VAL VAL GLY TYR SEQRES 7 A 436 ASP ARG ALA ARG ALA VAL LEU ALA ASP PRO ARG PHE SER SEQRES 8 A 436 LYS ASP TRP ARG ASN SER THR THR PRO LEU THR GLU ALA SEQRES 9 A 436 GLU ALA ALA LEU ASN HIS ASN MET LEU GLU SER ASP PRO SEQRES 10 A 436 PRO ARG HIS THR ARG LEU ARG LYS LEU VAL ALA ARG GLU SEQRES 11 A 436 PHE THR MET ARG ARG VAL GLU LEU LEU ARG PRO ARG VAL SEQRES 12 A 436 GLN GLU ILE VAL ASP GLY LEU VAL ASP ALA MET LEU ALA SEQRES 13 A 436 ALA PRO ASP GLY ARG ALA ASP LEU MET GLU SER LEU ALA SEQRES 14 A 436 TRP PRO LEU PRO ILE THR VAL ILE SER GLU LEU LEU GLY SEQRES 15 A 436 VAL PRO GLU PRO ASP ARG ALA ALA PHE ARG VAL TRP THR SEQRES 16 A 436 ASP ALA PHE VAL PHE PRO ASP ASP PRO ALA GLN ALA GLN SEQRES 17 A 436 THR ALA MET ALA GLU MET SER GLY TYR LEU SER ARG LEU SEQRES 18 A 436 ILE ASP SER LYS ARG GLY GLN ASP GLY GLU ASP LEU LEU SEQRES 19 A 436 SER ALA LEU VAL ARG THR SER ASP GLU ASP GLY SER ARG SEQRES 20 A 436 LEU THR SER GLU GLU LEU LEU GLY MET ALA HIS ILE LEU SEQRES 21 A 436 LEU VAL ALA GLY HIS GLU THR THR VAL ASN LEU ILE ALA SEQRES 22 A 436 ASN GLY MET TYR ALA LEU LEU SER HIS PRO ASP GLN LEU SEQRES 23 A 436 ALA ALA LEU ARG ALA ASP MET THR LEU LEU ASP GLY ALA SEQRES 24 A 436 VAL GLU GLU MET LEU ARG TYR GLU GLY PRO VAL GLU SER SEQRES 25 A 436 ALA THR TYR ARG PHE PRO VAL GLU PRO VAL ASP LEU ASP SEQRES 26 A 436 GLY THR VAL ILE PRO ALA GLY ASP THR VAL LEU VAL VAL SEQRES 27 A 436 LEU ALA ASP ALA HIS ARG THR PRO GLU ARG PHE PRO ASP SEQRES 28 A 436 PRO HIS ARG PHE ASP ILE ARG ARG ASP THR ALA GLY HIS SEQRES 29 A 436 LEU ALA PHE GLY HIS GLY ILE HIS PHE CYS ILE GLY ALA SEQRES 30 A 436 PRO LEU ALA ARG LEU GLU ALA ARG ILE ALA VAL ARG ALA SEQRES 31 A 436 LEU LEU GLU ARG CYS PRO ASP LEU ALA LEU ASP VAL SER SEQRES 32 A 436 PRO GLY GLU LEU VAL TRP TYR PRO ASN PRO MET ILE ARG SEQRES 33 A 436 GLY LEU LYS ALA LEU PRO ILE ARG TRP ARG ARG GLY ARG SEQRES 34 A 436 GLU ALA GLY ARG ARG THR GLY SEQRES 1 B 436 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 436 LEU VAL PRO ARG GLY SER HIS MET ARG ARG THR GLN GLN SEQRES 3 B 436 GLY THR THR ALA SER PRO PRO VAL LEU ASP LEU GLY ALA SEQRES 4 B 436 LEU GLY GLN ASP PHE ALA ALA ASP PRO TYR PRO THR TYR SEQRES 5 B 436 ALA ARG LEU ARG ALA GLU GLY PRO ALA HIS ARG VAL ARG SEQRES 6 B 436 THR PRO GLU GLY ASP GLU VAL TRP LEU VAL VAL GLY TYR SEQRES 7 B 436 ASP ARG ALA ARG ALA VAL LEU ALA ASP PRO ARG PHE SER SEQRES 8 B 436 LYS ASP TRP ARG ASN SER THR THR PRO LEU THR GLU ALA SEQRES 9 B 436 GLU ALA ALA LEU ASN HIS ASN MET LEU GLU SER ASP PRO SEQRES 10 B 436 PRO ARG HIS THR ARG LEU ARG LYS LEU VAL ALA ARG GLU SEQRES 11 B 436 PHE THR MET ARG ARG VAL GLU LEU LEU ARG PRO ARG VAL SEQRES 12 B 436 GLN GLU ILE VAL ASP GLY LEU VAL ASP ALA MET LEU ALA SEQRES 13 B 436 ALA PRO ASP GLY ARG ALA ASP LEU MET GLU SER LEU ALA SEQRES 14 B 436 TRP PRO LEU PRO ILE THR VAL ILE SER GLU LEU LEU GLY SEQRES 15 B 436 VAL PRO GLU PRO ASP ARG ALA ALA PHE ARG VAL TRP THR SEQRES 16 B 436 ASP ALA PHE VAL PHE PRO ASP ASP PRO ALA GLN ALA GLN SEQRES 17 B 436 THR ALA MET ALA GLU MET SER GLY TYR LEU SER ARG LEU SEQRES 18 B 436 ILE ASP SER LYS ARG GLY GLN ASP GLY GLU ASP LEU LEU SEQRES 19 B 436 SER ALA LEU VAL ARG THR SER ASP GLU ASP GLY SER ARG SEQRES 20 B 436 LEU THR SER GLU GLU LEU LEU GLY MET ALA HIS ILE LEU SEQRES 21 B 436 LEU VAL ALA GLY HIS GLU THR THR VAL ASN LEU ILE ALA SEQRES 22 B 436 ASN GLY MET TYR ALA LEU LEU SER HIS PRO ASP GLN LEU SEQRES 23 B 436 ALA ALA LEU ARG ALA ASP MET THR LEU LEU ASP GLY ALA SEQRES 24 B 436 VAL GLU GLU MET LEU ARG TYR GLU GLY PRO VAL GLU SER SEQRES 25 B 436 ALA THR TYR ARG PHE PRO VAL GLU PRO VAL ASP LEU ASP SEQRES 26 B 436 GLY THR VAL ILE PRO ALA GLY ASP THR VAL LEU VAL VAL SEQRES 27 B 436 LEU ALA ASP ALA HIS ARG THR PRO GLU ARG PHE PRO ASP SEQRES 28 B 436 PRO HIS ARG PHE ASP ILE ARG ARG ASP THR ALA GLY HIS SEQRES 29 B 436 LEU ALA PHE GLY HIS GLY ILE HIS PHE CYS ILE GLY ALA SEQRES 30 B 436 PRO LEU ALA ARG LEU GLU ALA ARG ILE ALA VAL ARG ALA SEQRES 31 B 436 LEU LEU GLU ARG CYS PRO ASP LEU ALA LEU ASP VAL SER SEQRES 32 B 436 PRO GLY GLU LEU VAL TRP TYR PRO ASN PRO MET ILE ARG SEQRES 33 B 436 GLY LEU LYS ALA LEU PRO ILE ARG TRP ARG ARG GLY ARG SEQRES 34 B 436 GLU ALA GLY ARG ARG THR GLY HET HEM A 419 43 HET PXI A 420 32 HET HEM B 419 43 HET PXI B 420 32 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PXI 4-{[4-(DIMETHYLAMINO)-3-HYDROXY-6-METHYLTETRAHYDRO-2H- HETNAM 2 PXI PYRAN-2-YL]OXY}-12-ETHYL-3,5,7,11- HETNAM 3 PXI TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 PXI 2(C25 H43 N O6) FORMUL 7 HOH *255(H2 O) HELIX 1 1 ASP A 16 ASP A 27 1 12 HELIX 2 2 PRO A 28 ALA A 37 1 10 HELIX 3 3 GLY A 57 ASP A 67 1 11 HELIX 4 4 ASP A 73 SER A 77 5 5 HELIX 5 5 ALA A 84 LEU A 88 5 5 HELIX 6 6 ASN A 91 SER A 95 5 5 HELIX 7 7 PRO A 98 ALA A 108 1 11 HELIX 8 8 ARG A 109 PHE A 111 5 3 HELIX 9 9 THR A 112 LEU A 118 1 7 HELIX 10 10 LEU A 119 ALA A 136 1 18 HELIX 11 11 LEU A 144 LEU A 148 1 5 HELIX 12 12 TRP A 150 GLY A 162 1 13 HELIX 13 13 PRO A 164 PRO A 166 5 3 HELIX 14 14 ASP A 167 PHE A 180 1 14 HELIX 15 15 ALA A 185 ARG A 206 1 22 HELIX 16 16 ASP A 212 ASP A 224 1 13 HELIX 17 17 THR A 229 ALA A 243 1 15 HELIX 18 18 GLY A 244 SER A 261 1 18 HELIX 19 19 HIS A 262 ASP A 272 1 11 HELIX 20 20 LEU A 275 GLY A 288 1 14 HELIX 21 21 VAL A 318 HIS A 323 1 6 HELIX 22 22 GLY A 356 ARG A 374 1 19 HELIX 23 23 SER A 383 LEU A 387 5 5 HELIX 24 24 LEU B 20 ASP B 27 1 8 HELIX 25 25 PRO B 28 GLY B 39 1 12 HELIX 26 26 GLY B 57 ASP B 67 1 11 HELIX 27 27 ASP B 73 SER B 77 5 5 HELIX 28 28 THR B 82 ALA B 87 1 6 HELIX 29 29 ASN B 91 SER B 95 5 5 HELIX 30 30 PRO B 98 ALA B 108 1 11 HELIX 31 31 ARG B 109 PHE B 111 5 3 HELIX 32 32 THR B 112 GLU B 117 1 6 HELIX 33 33 LEU B 119 LEU B 135 1 17 HELIX 34 34 LEU B 144 LEU B 148 1 5 HELIX 35 35 TRP B 150 LEU B 160 1 11 HELIX 36 36 PRO B 164 PRO B 166 5 3 HELIX 37 37 ASP B 167 PHE B 180 1 14 HELIX 38 38 ASP B 183 ARG B 206 1 24 HELIX 39 39 ASP B 212 ASP B 224 1 13 HELIX 40 40 THR B 229 ALA B 243 1 15 HELIX 41 41 HIS B 245 HIS B 262 1 18 HELIX 42 42 HIS B 262 ALA B 271 1 10 HELIX 43 43 ASP B 272 THR B 274 5 3 HELIX 44 44 LEU B 275 GLY B 288 1 14 HELIX 45 45 VAL B 318 HIS B 323 1 6 HELIX 46 46 GLY B 356 CYS B 375 1 20 SHEET 1 AA 3 ALA A 41 ARG A 45 0 SHEET 2 AA 3 GLU A 51 VAL A 55 -1 O VAL A 52 N VAL A 44 SHEET 3 AA 3 VAL A 315 VAL A 317 1 O LEU A 316 N VAL A 55 SHEET 1 AB 2 PHE A 70 SER A 71 0 SHEET 2 AB 2 PHE A 297 PRO A 298 -1 O PHE A 297 N SER A 71 SHEET 1 AC 3 ALA A 142 ASP A 143 0 SHEET 2 AC 3 PRO A 402 ARG A 404 -1 O ILE A 403 N ALA A 142 SHEET 3 AC 3 ALA A 379 LEU A 380 -1 O ALA A 379 N ARG A 404 SHEET 1 AD 2 VAL A 302 LEU A 304 0 SHEET 2 AD 2 THR A 307 ILE A 309 -1 O THR A 307 N LEU A 304 SHEET 1 BA 4 LEU B 15 ASP B 16 0 SHEET 2 BA 4 ALA B 41 ARG B 45 1 O ARG B 43 N LEU B 15 SHEET 3 BA 4 GLU B 51 VAL B 55 -1 O VAL B 52 N VAL B 44 SHEET 4 BA 4 VAL B 315 VAL B 317 1 O LEU B 316 N VAL B 55 SHEET 1 BB 2 PHE B 70 SER B 71 0 SHEET 2 BB 2 PHE B 297 PRO B 298 -1 O PHE B 297 N SER B 71 SHEET 1 BC 3 ARG B 141 ASP B 143 0 SHEET 2 BC 3 PRO B 402 ARG B 404 -1 O ILE B 403 N ALA B 142 SHEET 3 BC 3 ALA B 379 LEU B 380 -1 O ALA B 379 N ARG B 404 SHEET 1 BD 2 VAL B 302 LEU B 304 0 SHEET 2 BD 2 THR B 307 ILE B 309 -1 O THR B 307 N LEU B 304 LINK SG CYS A 354 FE HEM A 419 1555 1555 2.73 LINK SG CYS B 354 FE HEM B 419 1555 1555 2.90 CISPEP 1 PRO A 97 PRO A 98 0 0.20 CISPEP 2 PRO B 97 PRO B 98 0 0.03 SITE 1 AC1 25 LYS A 72 MET A 92 LEU A 93 HIS A 100 SITE 2 AC1 25 ARG A 104 PHE A 111 ALA A 243 GLY A 244 SITE 3 AC1 25 THR A 247 THR A 248 LEU A 251 ALA A 293 SITE 4 AC1 25 THR A 294 ARG A 296 ALA A 346 PHE A 347 SITE 5 AC1 25 GLY A 348 ILE A 351 HIS A 352 CYS A 354 SITE 6 AC1 25 ILE A 355 GLY A 356 LEU A 359 PXI A 420 SITE 7 AC1 25 HOH A2138 SITE 1 AC2 15 TRP A 74 GLU A 85 LEU A 88 ASN A 89 SITE 2 AC2 15 LEU A 93 GLU A 94 PHE A 178 VAL A 179 SITE 3 AC2 15 VAL A 242 ALA A 243 VAL A 290 SER A 292 SITE 4 AC2 15 THR A 294 HEM A 419 HOH A2139 SITE 1 AC3 24 MET B 92 LEU B 93 HIS B 100 ARG B 104 SITE 2 AC3 24 PHE B 111 LEU B 240 ALA B 243 GLY B 244 SITE 3 AC3 24 THR B 247 THR B 248 LEU B 251 PRO B 289 SITE 4 AC3 24 ALA B 293 THR B 294 ARG B 296 ALA B 346 SITE 5 AC3 24 ILE B 351 HIS B 352 CYS B 354 ILE B 355 SITE 6 AC3 24 GLY B 356 ALA B 360 PXI B 420 HOH B2102 SITE 1 AC4 16 GLU B 85 LEU B 88 ASN B 89 LEU B 93 SITE 2 AC4 16 GLU B 94 PHE B 178 VAL B 179 MET B 191 SITE 3 AC4 16 HIS B 238 VAL B 242 ALA B 243 GLU B 246 SITE 4 AC4 16 VAL B 290 THR B 294 ILE B 395 HEM B 419 CRYST1 58.401 92.102 67.574 90.00 89.99 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017123 0.000000 -0.000003 0.00000 SCALE2 0.000000 0.010858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014799 0.00000 MTRIX1 1 -0.997850 0.044820 0.047760 28.02234 1 MTRIX2 1 -0.043440 -0.998620 0.029580 -21.37904 1 MTRIX3 1 0.049020 0.027440 0.998420 -38.80744 1 (ATOM LINES ARE NOT SHOWN.) END