HEADER HYDROLASE 06-MAY-07 2Z00
TITLE CRYSTAL STRUCTURE OF DIHYDROOROTASE FROM THERMUS THERMOPHILUS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIHYDROOROTASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.5.2.3;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS;
SOURCE 3 ORGANISM_TAXID: 300852;
SOURCE 4 STRAIN: HB8;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-11A
KEYWDS ZINC BINDING PROTEIN, HYDROLASE, METAL-BINDING, PYRIMIDINE
KEYWDS 2 BIOSYNTHESIS, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON
KEYWDS 3 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL
KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI
EXPDTA X-RAY DIFFRACTION
AUTHOR M.KANAGAWA,S.BABA,S.KURAMITSU,S.YOKOYAMA,G.KAWAI,G.SAMPEI,RIKEN
AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 3 13-JUL-11 2Z00 1 VERSN
REVDAT 2 24-FEB-09 2Z00 1 VERSN
REVDAT 1 06-NOV-07 2Z00 0
JRNL AUTH M.KANAGAWA,S.BABA,S.KURAMITSU,S.YOKOYAMA,G.KAWAI,G.SAMPEI
JRNL TITL CRYSTAL STRUCTURE OF DIHYDROOROTASE FROM THERMUS
JRNL TITL 2 THERMOPHILUS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.42 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) : 2.42
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.85
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 71081.880
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5
REMARK 3 NUMBER OF REFLECTIONS : 39912
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) : 0.188
REMARK 3 FREE R VALUE : 0.192
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100
REMARK 3 FREE R VALUE TEST SET COUNT : 4017
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) : 2.42
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.70
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5622
REMARK 3 BIN R VALUE (WORKING SET) : 0.2200
REMARK 3 BIN FREE R VALUE : 0.2300
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 649
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 : 3224
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 2
REMARK 3 SOLVENT ATOMS : 393
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 22.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 3.14000
REMARK 3 B22 (A**2) : 3.14000
REMARK 3 B33 (A**2) : -6.28000
REMARK 3 B12 (A**2) : 3.57000
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) : 0.25
REMARK 3 ESD FROM SIGMAA (A) : 0.24
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) : 0.25
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.80
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.88
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) : 1.070 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.680 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.910 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.39
REMARK 3 BSOL : 39.90
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : ION.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2Z00 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-OCT-07.
REMARK 100 THE RCSB ID CODE IS RCSB027348.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-OCT-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL26B2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792, 0.9000, 0.9797
REMARK 200 MONOCHROMATOR : FIXED EXIT SI DOUBLE CRYSTAL
REMARK 200 MONOCHROMATOR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 297429
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.420
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 200 DATA REDUNDANCY : 2.800
REMARK 200 R MERGE (I) : 0.06700
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) : 2.42
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7
REMARK 200 DATA REDUNDANCY IN SHELL : 2.40
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: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 77.90
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.57
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 3.04M SODIUM CHLORIDE, 0.95M BIS-TRIS
REMARK 280 PROPANE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 139.93733
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 69.96867
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 104.95300
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.98433
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 174.92167
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 139.93733
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 69.96867
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.98433
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 104.95300
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 174.92167
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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2560 ANGSTROM**2
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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 209.90600
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A1364 LIES ON A SPECIAL POSITION.
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 58 O - C - N ANGL. DEV. = -10.0 DEGREES
REMARK 500 PRO A 117 C - N - CA ANGL. DEV. = -9.8 DEGREES
REMARK 500 GLY A 148 N - CA - C ANGL. DEV. = -19.5 DEGREES
REMARK 500 ARG A 149 CA - C - N ANGL. DEV. = -14.8 DEGREES
REMARK 500 ARG A 149 O - C - N ANGL. DEV. = 13.6 DEGREES
REMARK 500 THR A 150 C - N - CA ANGL. DEV. = -18.6 DEGREES
REMARK 500 THR A 150 CA - C - N ANGL. DEV. = 15.1 DEGREES
REMARK 500 ARG A 182 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES
REMARK 500 ASN A 183 C - N - CA ANGL. DEV. = -16.1 DEGREES
REMARK 500 HIS A 233 CA - C - O ANGL. DEV. = -14.8 DEGREES
REMARK 500 HIS A 233 CA - C - N ANGL. DEV. = 14.3 DEGREES
REMARK 500 HIS A 233 O - C - N ANGL. DEV. = -15.6 DEGREES
REMARK 500 LYS A 426 CB - CA - C ANGL. DEV. = -12.9 DEGREES
REMARK 500 LEU A 425 CA - C - N ANGL. DEV. = 14.8 DEGREES
REMARK 500 LEU A 425 O - C - N ANGL. DEV. = -16.2 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 59 30.57 39.59
REMARK 500 LEU A 112 -148.98 -114.32
REMARK 500 LYS A 124 16.54 52.37
REMARK 500 ASP A 147 130.22 -39.68
REMARK 500 ARG A 182 -126.45 45.74
REMARK 500 HIS A 233 96.97 -2.48
REMARK 500 ARG A 283 -160.25 -104.40
REMARK 500 HIS A 307 106.87 -56.33
REMARK 500 SER A 328 3.25 -163.75
REMARK 500 THR A 356 -92.73 -120.03
REMARK 500 SER A 400 137.15 -170.38
REMARK 500 ALA A 424 46.63 -148.56
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 LEU A 425 LYS A 426 -149.52
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG A 182 0.17 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 ARG A 59 -20.67
REMARK 500 ALA A 107 -10.44
REMARK 500 LEU A 112 26.84
REMARK 500 GLN A 232 -11.61
REMARK 500 HIS A 233 -32.48
REMARK 500 THR A 356 10.71
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A1260 DISTANCE = 6.11 ANGSTROMS
REMARK 525 HOH A1267 DISTANCE = 5.15 ANGSTROMS
REMARK 525 HOH A1308 DISTANCE = 5.29 ANGSTROMS
REMARK 525 HOH A1342 DISTANCE = 5.87 ANGSTROMS
REMARK 525 HOH A1386 DISTANCE = 5.03 ANGSTROMS
REMARK 525 HOH A1407 DISTANCE = 6.39 ANGSTROMS
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 ZN A1004 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 55 NE2
REMARK 620 2 HIS A 57 NE2 95.5
REMARK 620 3 ASP A 147 OD2 75.6 97.7
REMARK 620 4 ASP A 306 OD2 82.8 89.5 157.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1006 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 147 OD1
REMARK 620 2 HIS A 174 ND1 91.2
REMARK 620 3 HIS A 233 NE2 138.6 81.2
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1004
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1006
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: TTK003000118.1 RELATED DB: TARGETDB
DBREF 2Z00 A 1 426 UNP Q5SK67 Q5SK67_THET8 1 426
SEQRES 1 A 426 MSE ILE LEU ILE ARG ASN VAL ARG LEU VAL ASP ALA ARG
SEQRES 2 A 426 GLY GLU ARG GLY PRO ALA ASP VAL LEU ILE GLY GLU GLY
SEQRES 3 A 426 ARG ILE LEU SER LEU GLU GLY GLY GLU ALA LYS GLN VAL
SEQRES 4 A 426 VAL ASP GLY THR GLY CYS PHE LEU ALA PRO GLY PHE LEU
SEQRES 5 A 426 ASP LEU HIS ALA HIS LEU ARG GLU PRO GLY GLU GLU VAL
SEQRES 6 A 426 LYS GLU ASP LEU PHE SER GLY LEU LEU ALA ALA VAL ARG
SEQRES 7 A 426 GLY GLY TYR THR ASP LEU VAL SER MSE PRO ASN THR LYS
SEQRES 8 A 426 PRO PRO VAL ASP THR PRO GLU ALA VAL ARG ALA LEU LYS
SEQRES 9 A 426 GLU LYS ALA LYS ALA LEU GLY LEU ALA ARG LEU HIS PRO
SEQRES 10 A 426 ALA ALA ALA LEU THR GLU LYS GLN GLU GLY LYS THR LEU
SEQRES 11 A 426 THR PRO ALA GLY LEU LEU ARG GLU ALA GLY ALA VAL LEU
SEQRES 12 A 426 LEU THR ASP ASP GLY ARG THR ASN GLU ASP ALA GLY VAL
SEQRES 13 A 426 LEU ALA ALA GLY LEU LEU MSE ALA ALA PRO LEU GLY LEU
SEQRES 14 A 426 PRO VAL ALA VAL HIS ALA GLU ASP ALA GLY LEU ARG ARG
SEQRES 15 A 426 ASN GLY VAL MSE ASN ASP GLY PRO LEU ALA ASP LEU LEU
SEQRES 16 A 426 GLY LEU PRO GLY ASN PRO PRO GLU ALA GLU ALA ALA ARG
SEQRES 17 A 426 ILE ALA ARG ASP LEU GLU VAL LEU ARG TYR ALA LEU ARG
SEQRES 18 A 426 ARG SER PRO ALA THR PRO ARG LEU HIS VAL GLN HIS LEU
SEQRES 19 A 426 SER THR LYS ARG GLY LEU GLU LEU VAL ARG GLU ALA LYS
SEQRES 20 A 426 ARG ALA GLY LEU PRO VAL THR ALA GLU ALA THR PRO HIS
SEQRES 21 A 426 HIS LEU THR LEU THR GLU GLU ALA LEU ARG THR PHE ASP
SEQRES 22 A 426 PRO LEU PHE LYS VAL ALA PRO PRO LEU ARG GLY GLU GLU
SEQRES 23 A 426 ASP ARG GLU ALA LEU LEU GLU GLY LEU LEU ASP GLY THR
SEQRES 24 A 426 LEU ASP ALA ILE ALA THR ASP HIS ALA PRO HIS THR LEU
SEQRES 25 A 426 ALA GLU LYS GLU LYS ASP LEU LEU ARG ALA PRO PHE GLY
SEQRES 26 A 426 ILE PRO SER LEU GLU VAL ALA PHE PRO LEU LEU TYR THR
SEQRES 27 A 426 GLU LEU HIS LEU LYS ARG GLY PHE PRO LEU GLN ARG LEU
SEQRES 28 A 426 VAL GLU LEU PHE THR ASP GLY PRO ARG ARG VAL LEU GLY
SEQRES 29 A 426 LEU PRO PRO LEU HIS LEU GLU GLU GLY ALA GLU ALA SER
SEQRES 30 A 426 LEU VAL LEU LEU SER PRO LYS GLU ARG PRO VAL ASP PRO
SEQRES 31 A 426 SER ALA PHE ALA SER LYS ALA ARG TYR SER PRO TRP ALA
SEQRES 32 A 426 GLY TRP VAL LEU GLY GLY TRP PRO VAL LEU THR LEU VAL
SEQRES 33 A 426 ALA GLY ARG ILE VAL HIS GLU ALA LEU LYS
MODRES 2Z00 MSE A 1 MET SELENOMETHIONINE
MODRES 2Z00 MSE A 87 MET SELENOMETHIONINE
MODRES 2Z00 MSE A 163 MET SELENOMETHIONINE
MODRES 2Z00 MSE A 186 MET SELENOMETHIONINE
HET MSE A 1 8
HET MSE A 87 8
HET MSE A 163 8
HET MSE A 186 8
HET ZN A1004 1
HET ZN A1006 1
HETNAM MSE SELENOMETHIONINE
HETNAM ZN ZINC ION
FORMUL 1 MSE 4(C5 H11 N O2 SE)
FORMUL 2 ZN 2(ZN 2+)
FORMUL 4 HOH *393(H2 O)
HELIX 1 1 ASP A 68 GLY A 79 1 12
HELIX 2 2 THR A 96 GLY A 111 1 16
HELIX 3 3 THR A 122 GLU A 126 5 5
HELIX 4 4 PRO A 132 GLY A 140 1 9
HELIX 5 5 ASP A 153 ALA A 165 1 13
HELIX 6 6 PRO A 166 GLY A 168 5 3
HELIX 7 7 ASP A 177 ARG A 182 1 6
HELIX 8 8 GLY A 189 GLY A 196 1 8
HELIX 9 9 PRO A 201 SER A 223 1 23
HELIX 10 10 THR A 236 ALA A 249 1 14
HELIX 11 11 THR A 258 LEU A 264 1 7
HELIX 12 12 THR A 265 PHE A 272 5 8
HELIX 13 13 ASP A 273 LYS A 277 5 5
HELIX 14 14 GLY A 284 ASP A 297 1 14
HELIX 15 15 ALA A 313 LYS A 317 5 5
HELIX 16 16 VAL A 331 LEU A 340 1 10
HELIX 17 17 LEU A 340 GLY A 345 1 6
HELIX 18 18 PRO A 347 THR A 356 1 10
HELIX 19 19 THR A 356 GLY A 364 1 9
HELIX 20 20 ASP A 389 PHE A 393 5 5
SHEET 1 A 4 ARG A 27 SER A 30 0
SHEET 2 A 4 GLY A 14 GLY A 24 -1 N LEU A 22 O SER A 30
SHEET 3 A 4 ILE A 2 ASP A 11 -1 N ILE A 2 O ILE A 23
SHEET 4 A 4 GLN A 38 ASP A 41 1 O VAL A 40 N LEU A 3
SHEET 1 B 7 ARG A 27 SER A 30 0
SHEET 2 B 7 GLY A 14 GLY A 24 -1 N LEU A 22 O SER A 30
SHEET 3 B 7 ILE A 2 ASP A 11 -1 N ILE A 2 O ILE A 23
SHEET 4 B 7 PHE A 46 PRO A 49 1 O LEU A 47 N ARG A 8
SHEET 5 B 7 LEU A 378 SER A 382 -1 O LEU A 381 N PHE A 46
SHEET 6 B 7 TRP A 410 VAL A 416 -1 O VAL A 412 N LEU A 380
SHEET 7 B 7 ARG A 419 GLU A 423 -1 O HIS A 422 N THR A 414
SHEET 1 C 3 PHE A 51 ALA A 56 0
SHEET 2 C 3 TYR A 81 SER A 86 1 O VAL A 85 N ASP A 53
SHEET 3 C 3 ARG A 114 LEU A 115 1 O ARG A 114 N LEU A 84
SHEET 1 D 6 ALA A 118 ALA A 119 0
SHEET 2 D 6 LEU A 143 THR A 145 1 O LEU A 143 N ALA A 119
SHEET 3 D 6 VAL A 171 VAL A 173 1 O ALA A 172 N LEU A 144
SHEET 4 D 6 LEU A 229 VAL A 231 1 O HIS A 230 N VAL A 171
SHEET 5 D 6 VAL A 253 ALA A 257 1 O THR A 254 N VAL A 231
SHEET 6 D 6 ALA A 302 ILE A 303 1 O ALA A 302 N ALA A 257
SHEET 1 E 2 MSE A 186 ASN A 187 0
SHEET 2 E 2 GLY A 199 ASN A 200 1 O ASN A 200 N MSE A 186
SHEET 1 F 2 ARG A 386 PRO A 387 0
SHEET 2 F 2 VAL A 406 LEU A 407 -1 O LEU A 407 N ARG A 386
LINK NE2 HIS A 55 ZN ZN A1004 1555 1555 2.10
LINK NE2 HIS A 57 ZN ZN A1004 1555 1555 2.24
LINK OD1 ASP A 147 ZN ZN A1006 1555 1555 2.07
LINK OD2 ASP A 147 ZN ZN A1004 1555 1555 2.24
LINK ND1 HIS A 174 ZN ZN A1006 1555 1555 2.19
LINK NE2 HIS A 233 ZN ZN A1006 1555 1555 2.38
LINK OD2 ASP A 306 ZN ZN A1004 1555 1555 2.38
LINK C MSE A 1 N ILE A 2 1555 1555 1.33
LINK C SER A 86 N MSE A 87 1555 1555 1.32
LINK C MSE A 87 N PRO A 88 1555 1555 1.33
LINK C LEU A 162 N MSE A 163 1555 1555 1.33
LINK C MSE A 163 N ALA A 164 1555 1555 1.33
LINK C VAL A 185 N MSE A 186 1555 1555 1.34
LINK C MSE A 186 N ASN A 187 1555 1555 1.33
CISPEP 1 GLY A 17 PRO A 18 0 -0.13
CISPEP 2 GLU A 60 PRO A 61 0 0.37
CISPEP 3 LYS A 91 PRO A 92 0 -0.10
CISPEP 4 ALA A 279 PRO A 280 0 -0.28
SITE 1 AC1 5 HIS A 55 HIS A 57 ASP A 147 ASP A 306
SITE 2 AC1 5 ZN A1006
SITE 1 AC2 4 ASP A 147 HIS A 174 HIS A 233 ZN A1004
CRYST1 129.937 129.937 209.906 90.00 90.00 120.00 P 65 2 2 12
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 0.007696 0.004443 0.000000 0.00000
SCALE2 0.000000 0.008887 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004764 0.00000
HETATM 1 N MSE A 1 42.241 46.518 130.520 1.00 46.01 N
HETATM 2 CA MSE A 1 40.752 46.499 130.449 1.00 46.91 C
HETATM 3 C MSE A 1 40.259 47.135 129.159 1.00 43.29 C
HETATM 4 O MSE A 1 40.505 48.310 128.902 1.00 45.08 O
HETATM 5 CB MSE A 1 40.161 47.238 131.644 1.00 53.09 C
HETATM 6 CG MSE A 1 38.650 47.290 131.634 1.00 60.29 C
HETATM 7 SE MSE A 1 38.030 47.571 133.278 1.00 67.94 SE
HETATM 8 CE MSE A 1 38.192 45.945 133.942 1.00 68.03 C
(ATOM LINES ARE NOT SHOWN.)
END
