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HEADER HYDROLASE 16-MAR-11 3R3Y
TITLE CRYSTAL STRUCTURE OF THE FLUOROACETATE DEHALOGENASE RPA1163 -
TITLE 2 HIS280ASN/FLUOROACETATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: FLUOROACETATE DEHALOGENASE;
COMPND 3 CHAIN: A, B;
COMPND 4 EC: 3.8.1.3;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS;
SOURCE 3 ORGANISM_TAXID: 1076;
SOURCE 4 STRAIN: CGA009;
SOURCE 5 GENE: RPA1163;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P15TV-L
KEYWDS FACD, DEFLUORINASE, ALPHA/BETA HYDROLASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.W.Y.CHAN,A.F.YAKUNIN,E.A.EDWARDS,E.F.PAI
REVDAT 1 04-MAY-11 3R3Y 0
JRNL AUTH P.W.CHAN,A.F.YAKUNIN,E.A.EDWARDS,E.F.PAI
JRNL TITL MAPPING THE REACTION COORDINATES OF ENZYMATIC
JRNL TITL 2 DEFLUORINATION.
JRNL REF J.AM.CHEM.SOC. 2011
JRNL REFN ESSN 1520-5126
JRNL PMID 21510690
JRNL DOI 10.1021/JA200277D
REMARK 2
REMARK 2 RESOLUTION. 1.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
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) : 1.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.38
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6
REMARK 3 NUMBER OF REFLECTIONS : 172880
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) : 0.153
REMARK 3 R VALUE (WORKING SET) : 0.151
REMARK 3 FREE R VALUE : 0.187
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 8724
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) : 1.15
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.18
REMARK 3 REFLECTION IN BIN (WORKING SET) : 9519
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.18
REMARK 3 BIN R VALUE (WORKING SET) : 0.2070
REMARK 3 BIN FREE R VALUE SET COUNT : 501
REMARK 3 BIN FREE R VALUE : 0.2480
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4657
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 3
REMARK 3 SOLVENT ATOMS : 463
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 13.74
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.63
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.29000
REMARK 3 B22 (A**2) : 0.96000
REMARK 3 B33 (A**2) : -0.60000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.16000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.237
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4974 ; 0.026 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 3426 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6788 ; 2.196 ; 1.948
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8243 ; 1.251 ; 3.001
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 616 ; 6.466 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 233 ;34.993 ;22.532
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 755 ;13.091 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;16.663 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 688 ; 0.158 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5683 ; 0.015 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1112 ; 0.003 ; 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): 3032 ; 2.518 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1214 ; 0.910 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4864 ; 3.378 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1942 ; 4.636 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1924 ; 6.226 ; 4.500
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 8400 ; 2.087 ; 3.000
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 U VALUES: REFINED INDIVIDUALLY
REMARK 4
REMARK 4 3R3Y COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-11.
REMARK 100 THE RCSB ID CODE IS RCSB064458.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-APR-10
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 14-BM-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.978700
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 172884
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150
REMARK 200 RESOLUTION RANGE LOW (A) : 82.760
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.04900
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 15.2400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18
REMARK 200 COMPLETENESS FOR SHELL (%) : 71.2
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.17000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 3.350
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 (%): 38.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 15-24% PEG3350, 0.1-0.2M CACL2 AND
REMARK 280 0.1M TRIS-HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 298K
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 39.66500
REMARK 290 SMTRY3 2 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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2560 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20890 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A -1
REMARK 465 HIS A 0
REMARK 465 MET A 1
REMARK 465 PRO A 2
REMARK 465 ASP A 3
REMARK 465 ALA A 301
REMARK 465 PRO A 302
REMARK 465 GLY A 303
REMARK 465 SER A 304
REMARK 465 GLY B -1
REMARK 465 HIS B 0
REMARK 465 MET B 1
REMARK 465 PRO B 2
REMARK 465 ASP B 3
REMARK 465 ILE B 253
REMARK 465 ALA B 254
REMARK 465 GLN B 255
REMARK 465 SER B 256
REMARK 465 ALA B 257
REMARK 465 ALA B 258
REMARK 465 ALA B 300
REMARK 465 ALA B 301
REMARK 465 PRO B 302
REMARK 465 GLY B 303
REMARK 465 SER B 304
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 OH TYR A 149 CB ALA A 257 1.52
REMARK 500 O HOH A 371 O HOH A 434 1.96
REMARK 500 CE2 PHE B 176 O HOH B 439 2.00
REMARK 500 OD1 ASN A 168 O HOH A 501 2.13
REMARK 500 OE1 GLU A 277 O HOH A 538 2.14
REMARK 500 O HOH A 403 O HOH A 554 2.15
REMARK 500 CE2 PHE B 176 O HOH A 397 2.16
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 478 O HOH B 467 2656 2.18
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 VAL A 50 CB VAL A 50 CG2 -0.152
REMARK 500 GLU A 97 CB GLU A 97 CG -0.132
REMARK 500 TYR A 141 CZ TYR A 141 OH -0.155
REMARK 500 TYR A 149 CD1 TYR A 149 CE1 -0.115
REMARK 500 TRP B 15 CB TRP B 15 CG 0.136
REMARK 500 VAL B 50 CB VAL B 50 CG2 -0.127
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 ASP A 6 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ARG A 86 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES
REMARK 500 TYR A 224 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES
REMARK 500 MET A 244 CG - SD - CE ANGL. DEV. = -14.0 DEGREES
REMARK 500 ASP B 226 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 MET B 244 CG - SD - CE ANGL. DEV. = -13.3 DEGREES
REMARK 500 ARG B 296 NE - CZ - NH1 ANGL. DEV. = 3.1 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 PRO A 41 68.32 -103.42
REMARK 500 ASB A 110 -129.41 55.63
REMARK 500 MET A 145 71.07 -46.94
REMARK 500 ASP A 173 61.93 -152.75
REMARK 500 TYR A 224 -100.45 -121.86
REMARK 500 ALA A 257 49.47 -144.30
REMARK 500 PRO B 41 63.33 -102.26
REMARK 500 ASB B 110 -128.83 56.14
REMARK 500 MET B 145 72.63 -55.79
REMARK 500 ILE B 153 53.33 -115.53
REMARK 500 ASP B 173 72.21 -151.85
REMARK 500 TYR B 224 -96.21 -123.09
REMARK 500 ALA B 274 142.96 -170.39
REMARK 500 SER B 278 158.25 177.67
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 114 0.10 SIDE CHAIN
REMARK 500 TYR A 154 0.07 SIDE CHAIN
REMARK 500 ARG B 114 0.09 SIDE CHAIN
REMARK 500 TYR B 154 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 ILE A 253 23.8 L L OUTSIDE RANGE
REMARK 500 THR B 81 24.8 L L OUTSIDE RANGE
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 A 540 DISTANCE = 6.90 ANGSTROMS
REMARK 525 HOH A 552 DISTANCE = 6.73 ANGSTROMS
REMARK 525 HOH B 457 DISTANCE = 5.30 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 CA A 305 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 364 O
REMARK 620 2 GLN A 98 OE1 77.6
REMARK 620 N 1
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 305
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3R3U RELATED DB: PDB
REMARK 900 THE WT/APO CRYSTAL STRUCTURE.
REMARK 900 RELATED ID: 3R3V RELATED DB: PDB
REMARK 900 THE ASP110ASN MUTANT IN COMPLEX WITH FLUOROACETATE.
REMARK 900 RELATED ID: 3R3W RELATED DB: PDB
REMARK 900 THE ASP110ASN MUTANT IN COMPLEX WITH CHLOROACETATE.
REMARK 900 RELATED ID: 3R3X RELATED DB: PDB
REMARK 900 THE ASP110ASN MUTANT IN COMPLEX WITH BROMOACETATE.
REMARK 900 RELATED ID: 3R3Z RELATED DB: PDB
REMARK 900 THE WT IN COMPLEX WITH GLYCOLATE
REMARK 900 RELATED ID: 3R40 RELATED DB: PDB
REMARK 900 THE ASP110ASN MUTANT/APO CRYSTAL STRUCTURE
REMARK 900 RELATED ID: 3R41 RELATED DB: PDB
REMARK 900 THE HIS280ASN/APO CRYSTAL STRUCTURE
DBREF 3R3Y A 1 302 UNP Q6NAM1 DEHA_RHOPA 1 302
DBREF 3R3Y B 1 302 UNP Q6NAM1 DEHA_RHOPA 1 302
SEQADV 3R3Y GLY A -1 UNP Q6NAM1 EXPRESSION TAG
SEQADV 3R3Y HIS A 0 UNP Q6NAM1 EXPRESSION TAG
SEQADV 3R3Y ASN A 280 UNP Q6NAM1 HIS 280 ENGINEERED MUTATION
SEQADV 3R3Y GLY A 303 UNP Q6NAM1 EXPRESSION TAG
SEQADV 3R3Y SER A 304 UNP Q6NAM1 EXPRESSION TAG
SEQADV 3R3Y GLY B -1 UNP Q6NAM1 EXPRESSION TAG
SEQADV 3R3Y HIS B 0 UNP Q6NAM1 EXPRESSION TAG
SEQADV 3R3Y ASN B 280 UNP Q6NAM1 HIS 280 ENGINEERED MUTATION
SEQADV 3R3Y GLY B 303 UNP Q6NAM1 EXPRESSION TAG
SEQADV 3R3Y SER B 304 UNP Q6NAM1 EXPRESSION TAG
SEQRES 1 A 306 GLY HIS MET PRO ASP LEU ALA ASP LEU PHE PRO GLY PHE
SEQRES 2 A 306 GLY SER GLU TRP ILE ASN THR SER SER GLY ARG ILE PHE
SEQRES 3 A 306 ALA ARG VAL GLY GLY ASP GLY PRO PRO LEU LEU LEU LEU
SEQRES 4 A 306 HIS GLY PHE PRO GLN THR HIS VAL MET TRP HIS ARG VAL
SEQRES 5 A 306 ALA PRO LYS LEU ALA GLU ARG PHE LYS VAL ILE VAL ALA
SEQRES 6 A 306 ASP LEU PRO GLY TYR GLY TRP SER ASP MET PRO GLU SER
SEQRES 7 A 306 ASP GLU GLN HIS THR PRO TYR THR LYS ARG ALA MET ALA
SEQRES 8 A 306 LYS GLN LEU ILE GLU ALA MET GLU GLN LEU GLY HIS VAL
SEQRES 9 A 306 HIS PHE ALA LEU ALA GLY HIS ASB ARG GLY ALA ARG VAL
SEQRES 10 A 306 SER TYR ARG LEU ALA LEU ASP SER PRO GLY ARG LEU SER
SEQRES 11 A 306 LYS LEU ALA VAL LEU ASP ILE LEU PRO THR TYR GLU TYR
SEQRES 12 A 306 TRP GLN ARG MET ASN ARG ALA TYR ALA LEU LYS ILE TYR
SEQRES 13 A 306 HIS TRP SER PHE LEU ALA GLN PRO ALA PRO LEU PRO GLU
SEQRES 14 A 306 ASN LEU LEU GLY GLY ASP PRO ASP PHE TYR VAL LYS ALA
SEQRES 15 A 306 LYS LEU ALA SER TRP THR ARG ALA GLY ASP LEU SER ALA
SEQRES 16 A 306 PHE ASP PRO ARG ALA VAL GLU HIS TYR ARG ILE ALA PHE
SEQRES 17 A 306 ALA ASP PRO MET ARG ARG HIS VAL MET CYS GLU ASP TYR
SEQRES 18 A 306 ARG ALA GLY ALA TYR ALA ASP PHE GLU HIS ASP LYS ILE
SEQRES 19 A 306 ASP VAL GLU ALA GLY ASN LYS ILE PRO VAL PRO MET LEU
SEQRES 20 A 306 ALA LEU TRP GLY ALA SER GLY ILE ALA GLN SER ALA ALA
SEQRES 21 A 306 THR PRO LEU ASP VAL TRP ARG LYS TRP ALA SER ASP VAL
SEQRES 22 A 306 GLN GLY ALA PRO ILE GLU SER GLY ASN PHE LEU PRO GLU
SEQRES 23 A 306 GLU ALA PRO ASP GLN THR ALA GLU ALA LEU VAL ARG PHE
SEQRES 24 A 306 PHE SER ALA ALA PRO GLY SER
SEQRES 1 B 306 GLY HIS MET PRO ASP LEU ALA ASP LEU PHE PRO GLY PHE
SEQRES 2 B 306 GLY SER GLU TRP ILE ASN THR SER SER GLY ARG ILE PHE
SEQRES 3 B 306 ALA ARG VAL GLY GLY ASP GLY PRO PRO LEU LEU LEU LEU
SEQRES 4 B 306 HIS GLY PHE PRO GLN THR HIS VAL MET TRP HIS ARG VAL
SEQRES 5 B 306 ALA PRO LYS LEU ALA GLU ARG PHE LYS VAL ILE VAL ALA
SEQRES 6 B 306 ASP LEU PRO GLY TYR GLY TRP SER ASP MET PRO GLU SER
SEQRES 7 B 306 ASP GLU GLN HIS THR PRO TYR THR LYS ARG ALA MET ALA
SEQRES 8 B 306 LYS GLN LEU ILE GLU ALA MET GLU GLN LEU GLY HIS VAL
SEQRES 9 B 306 HIS PHE ALA LEU ALA GLY HIS ASB ARG GLY ALA ARG VAL
SEQRES 10 B 306 SER TYR ARG LEU ALA LEU ASP SER PRO GLY ARG LEU SER
SEQRES 11 B 306 LYS LEU ALA VAL LEU ASP ILE LEU PRO THR TYR GLU TYR
SEQRES 12 B 306 TRP GLN ARG MET ASN ARG ALA TYR ALA LEU LYS ILE TYR
SEQRES 13 B 306 HIS TRP SER PHE LEU ALA GLN PRO ALA PRO LEU PRO GLU
SEQRES 14 B 306 ASN LEU LEU GLY GLY ASP PRO ASP PHE TYR VAL LYS ALA
SEQRES 15 B 306 LYS LEU ALA SER TRP THR ARG ALA GLY ASP LEU SER ALA
SEQRES 16 B 306 PHE ASP PRO ARG ALA VAL GLU HIS TYR ARG ILE ALA PHE
SEQRES 17 B 306 ALA ASP PRO MET ARG ARG HIS VAL MET CYS GLU ASP TYR
SEQRES 18 B 306 ARG ALA GLY ALA TYR ALA ASP PHE GLU HIS ASP LYS ILE
SEQRES 19 B 306 ASP VAL GLU ALA GLY ASN LYS ILE PRO VAL PRO MET LEU
SEQRES 20 B 306 ALA LEU TRP GLY ALA SER GLY ILE ALA GLN SER ALA ALA
SEQRES 21 B 306 THR PRO LEU ASP VAL TRP ARG LYS TRP ALA SER ASP VAL
SEQRES 22 B 306 GLN GLY ALA PRO ILE GLU SER GLY ASN PHE LEU PRO GLU
SEQRES 23 B 306 GLU ALA PRO ASP GLN THR ALA GLU ALA LEU VAL ARG PHE
SEQRES 24 B 306 PHE SER ALA ALA PRO GLY SER
MODRES 3R3Y ASB A 110 ASP ASPARTIC ACID-4-CARBOXYMETHYL ESTER
MODRES 3R3Y ASB B 110 ASP ASPARTIC ACID-4-CARBOXYMETHYL ESTER
HET ASB A 110 12
HET ASB B 110 12
HET CA A 305 1
HET CL A 306 1
HET CL B 305 1
HETNAM ASB ASPARTIC ACID-4-CARBOXYMETHYL ESTER
HETNAM CA CALCIUM ION
HETNAM CL CHLORIDE ION
FORMUL 1 ASB 2(C6 H9 N O6)
FORMUL 3 CA CA 2+
FORMUL 4 CL 2(CL 1-)
FORMUL 6 HOH *463(H2 O)
HELIX 1 1 THR A 43 HIS A 48 5 6
HELIX 2 2 VAL A 50 GLU A 56 1 7
HELIX 3 3 HIS A 80 TYR A 83 5 4
HELIX 4 4 THR A 84 LEU A 99 1 16
HELIX 5 5 ASB A 110 SER A 123 1 14
HELIX 6 6 PRO A 137 ARG A 144 1 8
HELIX 7 7 ASN A 146 ILE A 153 1 8
HELIX 8 8 TYR A 154 LEU A 159 1 6
HELIX 9 9 PRO A 164 GLY A 171 1 8
HELIX 10 10 ASP A 173 TRP A 185 1 13
HELIX 11 11 ASP A 195 ALA A 207 1 13
HELIX 12 12 ASP A 208 TYR A 224 1 17
HELIX 13 13 TYR A 224 GLY A 237 1 14
HELIX 14 14 GLY A 252 SER A 256 5 5
HELIX 15 15 THR A 259 ALA A 268 1 10
HELIX 16 16 PHE A 281 ALA A 286 1 6
HELIX 17 17 ALA A 286 ALA A 300 1 15
HELIX 18 18 THR B 43 HIS B 48 5 6
HELIX 19 19 VAL B 50 ALA B 55 1 6
HELIX 20 20 HIS B 80 TYR B 83 5 4
HELIX 21 21 THR B 84 LEU B 99 1 16
HELIX 22 22 ASB B 110 SER B 123 1 14
HELIX 23 23 PRO B 137 ARG B 144 1 8
HELIX 24 24 ASN B 146 ILE B 153 1 8
HELIX 25 25 TYR B 154 LEU B 159 1 6
HELIX 26 26 PRO B 164 GLY B 171 1 8
HELIX 27 27 ASP B 173 TRP B 185 1 13
HELIX 28 28 ASP B 195 ALA B 207 1 13
HELIX 29 29 ASP B 208 TYR B 224 1 17
HELIX 30 30 TYR B 224 GLY B 237 1 14
HELIX 31 31 THR B 259 LYS B 266 1 8
HELIX 32 32 PHE B 281 ALA B 286 1 6
HELIX 33 33 ALA B 286 SER B 299 1 14
SHEET 1 A 8 GLY A 12 ILE A 16 0
SHEET 2 A 8 ILE A 23 GLY A 29 -1 O ILE A 23 N ILE A 16
SHEET 3 A 8 LYS A 59 ALA A 63 -1 O VAL A 62 N ARG A 26
SHEET 4 A 8 PRO A 33 LEU A 37 1 N LEU A 34 O LYS A 59
SHEET 5 A 8 PHE A 104 HIS A 109 1 O ALA A 105 N LEU A 35
SHEET 6 A 8 LEU A 127 LEU A 133 1 O ALA A 131 N LEU A 106
SHEET 7 A 8 MET A 244 GLY A 249 1 O LEU A 245 N VAL A 132
SHEET 8 A 8 VAL A 271 ILE A 276 1 O GLN A 272 N ALA A 246
SHEET 1 B 8 PHE B 11 ILE B 16 0
SHEET 2 B 8 ILE B 23 GLY B 29 -1 O VAL B 27 N GLY B 12
SHEET 3 B 8 LYS B 59 ALA B 63 -1 O VAL B 60 N GLY B 28
SHEET 4 B 8 PRO B 33 LEU B 37 1 N LEU B 34 O ILE B 61
SHEET 5 B 8 PHE B 104 HIS B 109 1 O ALA B 105 N LEU B 35
SHEET 6 B 8 LEU B 127 LEU B 133 1 O ALA B 131 N LEU B 106
SHEET 7 B 8 MET B 244 GLY B 249 1 O LEU B 245 N VAL B 132
SHEET 8 B 8 VAL B 271 ILE B 276 1 O ILE B 276 N TRP B 248
LINK C HIS A 109 N ASB A 110 1555 1555 1.37
LINK C ASB A 110 N ARG A 111 1555 1555 1.35
LINK C HIS B 109 N ASB B 110 1555 1555 1.35
LINK C ASB B 110 N ARG B 111 1555 1555 1.33
LINK CA CA A 305 O HOH A 364 1555 1555 2.36
LINK OE1 GLN A 98 CA CA A 305 1555 1555 2.40
CISPEP 1 PHE A 40 PRO A 41 0 -0.73
CISPEP 2 ALA A 163 PRO A 164 0 4.00
CISPEP 3 PHE B 40 PRO B 41 0 -0.86
CISPEP 4 ALA B 163 PRO B 164 0 6.84
SITE 1 AC1 4 GLN A 98 HOH A 364 HOH A 447 HOH A 537
SITE 1 AC2 4 ALA A 286 PRO A 287 ASP A 288 GLN A 289
SITE 1 AC3 2 ASN B 17 GLN B 98
CRYST1 41.760 79.330 85.010 90.00 103.20 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 0.023946 0.000000 0.005617 0.00000
SCALE2 0.000000 0.012606 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012083 0.00000
TER 2438 ALA A 300
TER 4808 SER B 299
MASTER 466 0 5 33 16 0 3 6 5123 2 31 48
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