HEADER TRANSFERASE 13-DEC-10 3PYG
TITLE MYCOBACTERIUM TUBERCULOSIS 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
TITLE 2 KINASE (ISPE) IN COMPLEX WITH ADP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ISPE, CMK, 4-(CYTIDINE-5'-DIPHOSPHO)-2-C-METHYL-D-ERYTHRITOL
COMPND 5 KINASE;
COMPND 6 EC: 2.7.1.148;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS;
SOURCE 3 ORGANISM_TAXID: 1773;
SOURCE 4 GENE: ISPE, RV1011, MT1040, MTCI237.28;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS KINASE, 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE,
KEYWDS 2 TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.SHAN,X.H.CHEN,T.LIU,H.C.ZHAO,Z.H.RAO,Z.Y.LOU
REVDAT 2 20-MAR-24 3PYG 1 REMARK
REVDAT 1 25-JAN-12 3PYG 0
JRNL AUTH S.SHAN,X.H.CHEN,T.LIU,H.C.ZHAO,Z.H.RAO,Z.Y.LOU
JRNL TITL THE STRUCTURAL BASIS FOR ANTI-TB DRUG DISCOVERY TARGETING OF
JRNL TITL 2 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE (ISPE)
JRNL TITL 3 FROM MYCOBACTERIUM TUBERCULOSIS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.99 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.18
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1
REMARK 3 NUMBER OF REFLECTIONS : 26161
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 + TEST SET) : 0.222
REMARK 3 R VALUE (WORKING SET) : 0.220
REMARK 3 FREE R VALUE : 0.263
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1390
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.99
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1853
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.79
REMARK 3 BIN R VALUE (WORKING SET) : 0.2900
REMARK 3 BIN FREE R VALUE SET COUNT : 93
REMARK 3 BIN FREE R VALUE : 0.3340
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2144
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 27
REMARK 3 SOLVENT ATOMS : 168
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.10
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.64000
REMARK 3 B22 (A**2) : -0.37000
REMARK 3 B33 (A**2) : -2.27000
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 OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.168
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.995
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2222 ; 0.025 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3040 ; 2.213 ; 1.993
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 7.376 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;29.842 ;23.176
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 328 ;20.779 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;18.041 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 361 ; 0.211 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1687 ; 0.010 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1478 ; 1.414 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2349 ; 2.530 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 744 ; 3.854 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 689 ; 6.171 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3PYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-DEC-10.
REMARK 100 THE DEPOSITION ID IS D_1000062967.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-SEP-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL17U
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 : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26350
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990
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 (%) : 95.0
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 61.41
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE (PH 7.5), 1.5M
REMARK 280 LI2SO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
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 25.59950
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.47900
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.56100
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.47900
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.59950
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.56100
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: PISA
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 1
REMARK 465 PRO A 2
REMARK 465 THR A 3
REMARK 465 ALA A 302
REMARK 465 PRO A 303
REMARK 465 THR A 304
REMARK 465 GLU A 305
REMARK 465 VAL A 306
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 NE ARG A 298 O HOH A 436 2.00
REMARK 500 NH1 ARG A 9 OE2 GLU A 43 2.03
REMARK 500 OD2 ASP A 273 O HOH A 455 2.06
REMARK 500
REMARK 500 REMARK: NULL
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 O HOH A 439 O HOH A 470 4545 2.19
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 LEU A 40 CB - CG - CD1 ANGL. DEV. = 12.6 DEGREES
REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES
REMARK 500 ARG A 298 NE - CZ - NH2 ANGL. DEV. = -3.7 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 ARG A 24 -151.48 -127.94
REMARK 500 SER A 39 34.13 -78.61
REMARK 500 ASP A 67 -151.80 -131.63
REMARK 500 PRO A 198 123.82 -36.36
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLY A 152 THR A 153 -144.87
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 307
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3PYD RELATED DB: PDB
REMARK 900 RELATED ID: 3PYE RELATED DB: PDB
REMARK 900 RELATED ID: 3PYF RELATED DB: PDB
DBREF 3PYG A 1 306 UNP P65178 ISPE_MYCTU 1 306
SEQRES 1 A 306 MET PRO THR GLY SER VAL THR VAL ARG VAL PRO GLY LYS
SEQRES 2 A 306 VAL ASN LEU TYR LEU ALA VAL GLY ASP ARG ARG GLU ASP
SEQRES 3 A 306 GLY TYR HIS GLU LEU THR THR VAL PHE HIS ALA VAL SER
SEQRES 4 A 306 LEU VAL ASP GLU VAL THR VAL ARG ASN ALA ASP VAL LEU
SEQRES 5 A 306 SER LEU GLU LEU VAL GLY GLU GLY ALA ASP GLN LEU PRO
SEQRES 6 A 306 THR ASP GLU ARG ASN LEU ALA TRP GLN ALA ALA GLU LEU
SEQRES 7 A 306 MET ALA GLU HIS VAL GLY ARG ALA PRO ASP VAL SER ILE
SEQRES 8 A 306 MET ILE ASP LYS SER ILE PRO VAL ALA GLY GLY MET ALA
SEQRES 9 A 306 GLY GLY SER ALA ASP ALA ALA ALA VAL LEU VAL ALA MET
SEQRES 10 A 306 ASN SER LEU TRP GLU LEU ASN VAL PRO ARG ARG ASP LEU
SEQRES 11 A 306 ARG MET LEU ALA ALA ARG LEU GLY SER ASP VAL PRO PHE
SEQRES 12 A 306 ALA LEU HIS GLY GLY THR ALA LEU GLY THR GLY ARG GLY
SEQRES 13 A 306 GLU GLU LEU ALA THR VAL LEU SER ARG ASN THR PHE HIS
SEQRES 14 A 306 TRP VAL LEU ALA PHE ALA ASP SER GLY LEU LEU THR SER
SEQRES 15 A 306 ALA VAL TYR ASN GLU LEU ASP ARG LEU ARG GLU VAL GLY
SEQRES 16 A 306 ASP PRO PRO ARG LEU GLY GLU PRO GLY PRO VAL LEU ALA
SEQRES 17 A 306 ALA LEU ALA ALA GLY ASP PRO ASP GLN LEU ALA PRO LEU
SEQRES 18 A 306 LEU GLY ASN GLU MET GLN ALA ALA ALA VAL SER LEU ASP
SEQRES 19 A 306 PRO ALA LEU ALA ARG ALA LEU ARG ALA GLY VAL GLU ALA
SEQRES 20 A 306 GLY ALA LEU ALA GLY ILE VAL SER GLY SER GLY PRO THR
SEQRES 21 A 306 CYS ALA PHE LEU CYS THR SER ALA SER SER ALA ILE ASP
SEQRES 22 A 306 VAL GLY ALA GLN LEU SER GLY ALA GLY VAL CYS ARG THR
SEQRES 23 A 306 VAL ARG VAL ALA THR GLY PRO VAL PRO GLY ALA ARG VAL
SEQRES 24 A 306 VAL SER ALA PRO THR GLU VAL
HET ADP A 307 27
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
FORMUL 2 ADP C10 H15 N5 O10 P2
FORMUL 3 HOH *168(H2 O)
HELIX 1 1 GLY A 60 LEU A 64 5 5
HELIX 2 2 ASN A 70 VAL A 83 1 14
HELIX 3 3 ALA A 104 TRP A 121 1 18
HELIX 4 4 PRO A 126 GLY A 138 1 13
HELIX 5 5 ASP A 140 GLY A 147 1 8
HELIX 6 6 LEU A 180 GLY A 195 1 16
HELIX 7 7 PRO A 203 GLY A 213 1 11
HELIX 8 8 ASP A 214 ALA A 219 1 6
HELIX 9 9 PRO A 220 LEU A 222 5 3
HELIX 10 10 MET A 226 ASP A 234 1 9
HELIX 11 11 PRO A 235 ALA A 247 1 13
HELIX 12 12 SER A 267 ALA A 281 1 15
SHEET 1 A 5 SER A 53 VAL A 57 0
SHEET 2 A 5 VAL A 89 ASP A 94 1 O ILE A 93 N GLU A 55
SHEET 3 A 5 LEU A 31 ASN A 48 -1 N GLU A 43 O ASP A 94
SHEET 4 A 5 SER A 5 VAL A 20 -1 N VAL A 8 O VAL A 44
SHEET 5 A 5 GLY A 223 ASN A 224 1 O GLY A 223 N LEU A 16
SHEET 1 B 5 LEU A 159 VAL A 162 0
SHEET 2 B 5 THR A 149 GLY A 152 -1 N THR A 149 O VAL A 162
SHEET 3 B 5 LEU A 31 ASN A 48 -1 N THR A 33 O GLY A 152
SHEET 4 B 5 SER A 5 VAL A 20 -1 N VAL A 8 O VAL A 44
SHEET 5 B 5 ARG A 298 VAL A 299 -1 O ARG A 298 N ARG A 9
SHEET 1 C 4 ALA A 251 VAL A 254 0
SHEET 2 C 4 CYS A 261 CYS A 265 -1 O ALA A 262 N ILE A 253
SHEET 3 C 4 PHE A 168 PHE A 174 -1 N ALA A 173 O CYS A 261
SHEET 4 C 4 THR A 286 GLY A 292 -1 O GLY A 292 N PHE A 168
CISPEP 1 GLU A 25 ASP A 26 0 -1.23
CISPEP 2 GLY A 258 PRO A 259 0 13.22
CISPEP 3 GLY A 292 PRO A 293 0 -2.62
SITE 1 AC1 9 VAL A 99 ALA A 100 GLY A 101 GLY A 102
SITE 2 AC1 9 MET A 103 ALA A 104 GLY A 105 GLY A 106
SITE 3 AC1 9 HOH A 361
CRYST1 51.199 73.122 106.958 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 0.019532 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013676 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009349 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
