| 3V1M-pdb | HEADER HYDROLASE 09-DEC-11 3V1M
TITLE CRYSTAL STRUCTURE OF THE S112A/H265Q MUTANT OF A C-C HYDROLASE, BPHD
TITLE 2 FROM BURKHOLDERIA XENOVORANS LB400, AFTER EXPOSURE TO ITS SUBSTRATE
TITLE 3 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 3V1M 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. 1.92 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) : 1.92
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.79
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 23191
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) : 0.182
REMARK 3 R VALUE (WORKING SET) : 0.180
REMARK 3 FREE R VALUE : 0.225
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1189
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) : 1.92
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1421
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60
REMARK 3 BIN R VALUE (WORKING SET) : 0.2560
REMARK 3 BIN FREE R VALUE SET COUNT : 78
REMARK 3 BIN FREE R VALUE : 0.3050
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2238
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 23
REMARK 3 SOLVENT ATOMS : 121
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.77
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.90000
REMARK 3 B22 (A**2) : 0.90000
REMARK 3 B33 (A**2) : -1.79000
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): 0.159
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.516
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2415 ; 0.008 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1642 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3279 ; 1.172 ; 1.950
REMARK 3 BOND ANGLES OTHERS (DEGREES): 3979 ; 0.837 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 5.366 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;36.977 ;23.826
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 397 ;13.812 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.384 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.065 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2765 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 544 ; 0.002 ; 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 3V1M 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 RCSB069480.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-DEC-09
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
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 : C(111)
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 : 23211
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920
REMARK 200 RESOLUTION RANGE LOW (A) : 82.790
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 8.100
REMARK 200 R MERGE (I) : 0.07500
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 10.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0
REMARK 200 DATA REDUNDANCY IN SHELL : 5.00
REMARK 200 R MERGE FOR SHELL (I) : 0.38900
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 (%): 47.24
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M SODIUM MALONATE, PH 7.0, VAPOR
REMARK 280 DIFFUSING, SITTING DROP, MICROSEEDING, 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 58.54250
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 58.54250
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.59350
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 58.54250
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.79675
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 58.54250
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.39025
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 58.54250
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.39025
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.54250
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.79675
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 58.54250
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 58.54250
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.59350
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 58.54250
REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 58.54250
REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 43.59350
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 58.54250
REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 65.39025
REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 58.54250
REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 21.79675
REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 58.54250
REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 21.79675
REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 58.54250
REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 65.39025
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 58.54250
REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 58.54250
REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 43.59350
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: 11340 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 37740 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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: 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 ND2 ASN A 111 OE1 GLN A 265 2.11
REMARK 500 O ARG A 105 O HOH A 379 2.12
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 -119.41 34.22
REMARK 500 ASN A 75 -124.01 49.83
REMARK 500 ALA A 112 -117.55 59.52
REMARK 500 LEU A 140 34.56 -90.96
REMARK 500 TRP A 266 75.05 -100.81
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 WATER 379 MAY BE A CATION SUCH AS NA+ BUT THIS WAS NOT TESTED
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 287
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HPK A 288
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: 3V1N RELATED DB: PDB
DBREF 3V1M A 1 286 UNP P47229 BPHD_BURXL 1 286
SEQADV 3V1M ALA A 112 UNP P47229 SER 112 ENGINEERED MUTATION
SEQADV 3V1M 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 ALA 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 MLI A 287 7
HET HPK A 288 16
HETNAM MLI MALONATE ION
HETNAM HPK (3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE
FORMUL 2 MLI C3 H2 O4 2-
FORMUL 3 HPK C12 H9 O4 1-
FORMUL 4 HOH *121(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 LEU A 101 1 17
HELIX 5 5 ALA 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 ARG A 65 LYS A 69 -1 O LEU A 68 N ASN A 28
SHEET 4 A 8 THR A 35 LEU A 39 1 N VAL A 36 O ARG A 65
SHEET 5 A 8 ALA A 106 ASN A 111 1 O HIS A 107 N ILE A 37
SHEET 6 A 8 ILE A 129 MET A 135 1 O ILE A 133 N LEU A 108
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
CISPEP 1 MET A 148 PRO A 149 0 5.54
SITE 1 AC1 12 GLU A 34 THR A 35 ARG A 65 ILE A 103
SITE 2 AC1 12 ASP A 104 ARG A 105 SER A 180 ILE A 182
SITE 3 AC1 12 HOH A 316 HOH A 379 HOH A 391 HOH A 392
SITE 1 AC2 13 GLY A 41 GLY A 42 GLY A 43 ALA A 46
SITE 2 AC2 13 ALA A 112 MET A 113 ILE A 153 PHE A 175
SITE 3 AC2 13 ARG A 190 VAL A 240 TRP A 266 HOH A 374
SITE 4 AC2 13 HOH A 399
CRYST1 117.085 117.085 87.187 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 0.008541 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008541 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011470 0.00000
TER 2323 ALA A 286
MASTER 364 0 2 15 8 0 7 6 2382 1 23 22
END
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