| 3V1N-pdb | HEADER HYDROLASE 09-DEC-11 3V1N
TITLE CRYSTAL STRUCTURE OF THE H265Q MUTANT OF A C-C HYDROLASE, BPHD FROM
TITLE 2 BURKHOLDERIA XENOVORANS LB400, AFTER EXPOSURE TO ITS SUBSTRATE HOPDA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: HOPDA HYDROLASE, 2,6-DIOXO-6-PHENYLHEXA-3-ENOATE HYDROLASE;
COMPND 5 EC: 3.7.1.8;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA XENOVORANS;
SOURCE 3 ORGANISM_TAXID: 266265;
SOURCE 4 STRAIN: LB400;
SOURCE 5 GENE: BPHD, BXENO_C1120, BXE_C1186;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5A;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS C-C BOND HYDROLASE, ALPHA/BETA HYDROLASE FOLD, BPHD, ALPHA/BETA
KEYWDS 2 HYDROLASE, PCB DEGRADATION, META CLEAVAGE PRODUCT HYDROLASE, MCP
KEYWDS 3 HYDROLASE, 2-HYDROXY-6-OXO-6-PHENYL-HEXA-2,4-DIENOATE HYDROLASE,
KEYWDS 4 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.GHOSH,J.T.BOLIN
REVDAT 1 21-MAR-12 3V1N 0
JRNL AUTH A.C.RUZZINI,S.GHOSH,G.P.HORSMAN,L.J.FOSTER,J.T.BOLIN,
JRNL AUTH 2 L.D.ELTIS
JRNL TITL IDENTIFICATION OF AN ACYL-ENZYME INTERMEDIATE IN A
JRNL TITL 2 META-CLEAVAGE PRODUCT HYDROLASE REVEALS THE VERSATILITY OF
JRNL TITL 3 THE CATALYTIC TRIAD.
JRNL REF J.AM.CHEM.SOC. 2012
JRNL REFN ESSN 1520-5126
JRNL PMID 22339283
JRNL DOI 10.1021/JA208544G
REMARK 2
REMARK 2 RESOLUTION. 1.59 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.6.0117
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.48
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 40814
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) : 0.187
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.216
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2046
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) : 1.59
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.63
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2627
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50
REMARK 3 BIN R VALUE (WORKING SET) : 0.2960
REMARK 3 BIN FREE R VALUE SET COUNT : 149
REMARK 3 BIN FREE R VALUE : 0.3170
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2239
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 31
REMARK 3 SOLVENT ATOMS : 176
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.60
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.66000
REMARK 3 B22 (A**2) : 0.66000
REMARK 3 B33 (A**2) : -1.32000
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): 0.088
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.747
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2375 ; 0.011 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1621 ; 0.005 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3220 ; 1.387 ; 1.964
REMARK 3 BOND ANGLES OTHERS (DEGREES): 3934 ; 0.947 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ; 5.672 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;36.594 ;23.909
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 398 ;13.321 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.279 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 334 ; 0.075 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2703 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 522 ; 0.007 ; 0.020
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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 1.20
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; U VALUES: REFINED INDIVIDUALLY
REMARK 4
REMARK 4 3V1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-11.
REMARK 100 THE RCSB ID CODE IS RCSB069481.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-FEB-10
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 6.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 23-ID-D
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40851
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590
REMARK 200 RESOLUTION RANGE LOW (A) : 82.480
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 14.000
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 11.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7
REMARK 200 DATA REDUNDANCY IN SHELL : 11.10
REMARK 200 R MERGE FOR SHELL (I) : 0.82400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
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 (%): 47.06
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M SODIUM MALONATE, 10 MM CALCIUM
REMARK 280 CHLORIDE DIHYDRATE, PH 6.4, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 3555 -Y,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X,Z+3/4
REMARK 290 5555 -X+1/2,Y,-Z+3/4
REMARK 290 6555 X,-Y+1/2,-Z+1/4
REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2
REMARK 290 8555 -Y,-X,-Z
REMARK 290 9555 X+1/2,Y+1/2,Z+1/2
REMARK 290 10555 -X,-Y,Z
REMARK 290 11555 -Y+1/2,X,Z+3/4
REMARK 290 12555 Y,-X+1/2,Z+1/4
REMARK 290 13555 -X,Y+1/2,-Z+1/4
REMARK 290 14555 X+1/2,-Y,-Z+3/4
REMARK 290 15555 Y,X,-Z
REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2
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 58.32050
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 58.32050
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.79550
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 58.32050
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.89775
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 58.32050
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.69325
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 58.32050
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.69325
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.32050
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.89775
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 58.32050
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 58.32050
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.79550
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 58.32050
REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 58.32050
REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 43.79550
REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 58.32050
REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 65.69325
REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 58.32050
REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 21.89775
REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 58.32050
REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 21.89775
REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 58.32050
REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 65.69325
REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 58.32050
REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 58.32050
REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 43.79550
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 12620 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 37650 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL
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 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT3 4 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 THR A 2
REMARK 465 ALA A 3
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 HIS A 200 CG HIS A 200 CD2 0.063
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 LYS A 18 -119.67 46.59
REMARK 500 ASN A 75 -123.32 46.83
REMARK 500 SER A 112 -111.17 57.31
REMARK 500 LEU A 140 35.59 -89.87
REMARK 500 TRP A 266 72.95 -115.85
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 MLA A 287
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEZ A 288
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HPK A 289
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2OG1 RELATED DB: PDB
REMARK 900 BPHD WILD TYPE
REMARK 900 RELATED ID: 2RI6 RELATED DB: PDB
REMARK 900 BPHD S112A MUTANT
REMARK 900 RELATED ID: 2PU7 RELATED DB: PDB
REMARK 900 BPHD S112A/H265A MUTANT
REMARK 900 RELATED ID: 2PUH RELATED DB: PDB
REMARK 900 BPHD S112A MUTANT IN COMPLEX WITH SUBSTRATE HOPDA
REMARK 900 RELATED ID: 2PUJ RELATED DB: PDB
REMARK 900 BPHD S112A/H265Q MUTANT IN COMPLEX WITH SUBSTRATE HOPDA
REMARK 900 RELATED ID: 2RHW RELATED DB: PDB
REMARK 900 BPHD S112A MUTANT IN COMPLEX WITH 3, 10 - DIFLUORO HOPDA
REMARK 900 RELATED ID: 2RHT RELATED DB: PDB
REMARK 900 BPHD S112A MUTANT IN COMPLEX WITH 3-CL HOPDA
REMARK 900 RELATED ID: 3V1K RELATED DB: PDB
REMARK 900 RELATED ID: 3V1L RELATED DB: PDB
REMARK 900 RELATED ID: 3V1M RELATED DB: PDB
DBREF 3V1N A 1 286 UNP P47229 BPHD_BURXL 1 286
SEQADV 3V1N GLN A 265 UNP P47229 HIS 265 ENGINEERED MUTATION
SEQRES 1 A 286 MET THR ALA LEU THR GLU SER SER THR SER LYS PHE VAL
SEQRES 2 A 286 LYS ILE ASN GLU LYS GLY PHE SER ASP PHE ASN ILE HIS
SEQRES 3 A 286 TYR ASN GLU ALA GLY ASN GLY GLU THR VAL ILE MET LEU
SEQRES 4 A 286 HIS GLY GLY GLY PRO GLY ALA GLY GLY TRP SER ASN TYR
SEQRES 5 A 286 TYR ARG ASN VAL GLY PRO PHE VAL ASP ALA GLY TYR ARG
SEQRES 6 A 286 VAL ILE LEU LYS ASP SER PRO GLY PHE ASN LYS SER ASP
SEQRES 7 A 286 ALA VAL VAL MET ASP GLU GLN ARG GLY LEU VAL ASN ALA
SEQRES 8 A 286 ARG ALA VAL LYS GLY LEU MET ASP ALA LEU ASP ILE ASP
SEQRES 9 A 286 ARG ALA HIS LEU VAL GLY ASN SER MET GLY GLY ALA THR
SEQRES 10 A 286 ALA LEU ASN PHE ALA LEU GLU TYR PRO ASP ARG ILE GLY
SEQRES 11 A 286 LYS LEU ILE LEU MET GLY PRO GLY GLY LEU GLY PRO SER
SEQRES 12 A 286 MET PHE ALA PRO MET PRO MET GLU GLY ILE LYS LEU LEU
SEQRES 13 A 286 PHE LYS LEU TYR ALA GLU PRO SER TYR GLU THR LEU LYS
SEQRES 14 A 286 GLN MET LEU GLN VAL PHE LEU TYR ASP GLN SER LEU ILE
SEQRES 15 A 286 THR GLU GLU LEU LEU GLN GLY ARG TRP GLU ALA ILE GLN
SEQRES 16 A 286 ARG GLN PRO GLU HIS LEU LYS ASN PHE LEU ILE SER ALA
SEQRES 17 A 286 GLN LYS ALA PRO LEU SER THR TRP ASP VAL THR ALA ARG
SEQRES 18 A 286 LEU GLY GLU ILE LYS ALA LYS THR PHE ILE THR TRP GLY
SEQRES 19 A 286 ARG ASP ASP ARG PHE VAL PRO LEU ASP HIS GLY LEU LYS
SEQRES 20 A 286 LEU LEU TRP ASN ILE ASP ASP ALA ARG LEU HIS VAL PHE
SEQRES 21 A 286 SER LYS CYS GLY GLN TRP ALA GLN TRP GLU HIS ALA ASP
SEQRES 22 A 286 GLU PHE ASN ARG LEU VAL ILE ASP PHE LEU ARG HIS ALA
HET MLA A 287 7
HET BEZ A 288 8
HET HPK A 289 16
HETNAM MLA MALONIC ACID
HETNAM BEZ BENZOIC ACID
HETNAM HPK (3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE
HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID;
HETSYN 2 MLA METAHNEDICARBOXYLIC ACID
FORMUL 2 MLA C3 H4 O4
FORMUL 3 BEZ C7 H6 O2
FORMUL 4 HPK C12 H9 O4 1-
FORMUL 5 HOH *176(H2 O)
HELIX 1 1 THR A 5 THR A 9 1 5
HELIX 2 2 GLY A 47 TYR A 53 1 7
HELIX 3 3 ASN A 55 ALA A 62 1 8
HELIX 4 4 GLN A 85 ASP A 102 1 18
HELIX 5 5 SER A 112 TYR A 125 1 14
HELIX 6 6 MET A 150 GLU A 162 1 13
HELIX 7 7 SER A 164 LEU A 176 1 13
HELIX 8 8 ASP A 178 ILE A 182 5 5
HELIX 9 9 THR A 183 GLN A 197 1 15
HELIX 10 10 GLN A 197 ALA A 211 1 15
HELIX 11 11 PRO A 212 ASP A 217 5 6
HELIX 12 12 VAL A 218 ILE A 225 5 8
HELIX 13 13 LEU A 242 ILE A 252 1 11
HELIX 14 14 TRP A 266 HIS A 271 1 6
HELIX 15 15 HIS A 271 ALA A 286 1 16
SHEET 1 A 8 SER A 10 GLU A 17 0
SHEET 2 A 8 PHE A 20 ALA A 30 -1 O PHE A 23 N ILE A 15
SHEET 3 A 8 TYR A 64 LYS A 69 -1 O LEU A 68 N ASN A 28
SHEET 4 A 8 GLU A 34 LEU A 39 1 N MET A 38 O ILE A 67
SHEET 5 A 8 ALA A 106 ASN A 111 1 O VAL A 109 N LEU A 39
SHEET 6 A 8 ILE A 129 MET A 135 1 O MET A 135 N GLY A 110
SHEET 7 A 8 THR A 229 GLY A 234 1 O THR A 232 N LEU A 134
SHEET 8 A 8 ALA A 255 PHE A 260 1 O ARG A 256 N ILE A 231
LINK OG SER A 112 C BEZ A 288 1555 1555 1.42
CISPEP 1 MET A 148 PRO A 149 0 10.76
SITE 1 AC1 13 GLU A 34 THR A 35 ARG A 65 ASP A 102
SITE 2 AC1 13 ILE A 103 ASP A 104 ARG A 105 SER A 180
SITE 3 AC1 13 ILE A 182 HOH A 297 HOH A 356 HOH A 425
SITE 4 AC1 13 HOH A 443
SITE 1 AC2 7 GLY A 41 GLY A 42 SER A 112 MET A 113
SITE 2 AC2 7 ILE A 153 LEU A 213 VAL A 240
SITE 1 AC3 13 HIS A 40 GLY A 41 ALA A 46 GLY A 47
SITE 2 AC3 13 SER A 50 ASN A 51 LEU A 176 LEU A 181
SITE 3 AC3 13 LEU A 186 ARG A 190 TRP A 266 HOH A 440
SITE 4 AC3 13 HOH A 455
CRYST1 116.641 116.641 87.591 90.00 90.00 90.00 I 41 2 2 16
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 0.008573 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008573 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011417 0.00000
TER 2281 ALA A 286
MASTER 374 0 3 15 8 0 10 6 2446 1 32 22
END
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