HEADER LIGASE 15-DEC-11 3V4Z
TITLE D-ALANINE--D-ALANINE LIGASE FROM YERSINIA PESTIS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: D-ALANINE--D-ALANINE LIGASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: D-ALA-D-ALA LIGASE, D-ALANYLALANINE SYNTHETASE;
COMPND 5 EC: 6.3.2.4;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS;
SOURCE 3 ORGANISM_TAXID: 214092;
SOURCE 4 STRAIN: CO92;
SOURCE 5 GENE: DDL, DDLB, Y3624, YPO0557, YP_3627;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7
KEYWDS STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS
KEYWDS 2 DISEASES, CSGID, PEPTIDOGLYCAN SYNTHESIS, LIGASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.OSIPIUK,B.NOCEK,R.MULLIGAN,L.PAPAZISI,W.F.ANDERSON,A.JOACHIMIAK,
AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID)
REVDAT 1 28-DEC-11 3V4Z 0
JRNL AUTH J.OSIPIUK,B.NOCEK,R.MULLIGAN,L.PAPAZISI,W.F.ANDERSON,
JRNL AUTH 2 A.JOACHIMIAK
JRNL TITL D-ALANINE--D-ALANINE LIGASE FROM YERSINIA PESTIS.
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.69 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) : 2.69
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.70
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 18203
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) : 0.209
REMARK 3 R VALUE (WORKING SET) : 0.205
REMARK 3 FREE R VALUE : 0.289
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 927
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) : 2.69
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1141
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83
REMARK 3 BIN R VALUE (WORKING SET) : 0.3010
REMARK 3 BIN FREE R VALUE SET COUNT : 69
REMARK 3 BIN FREE R VALUE : 0.5030
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4399
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 17
REMARK 3 SOLVENT ATOMS : 23
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 70.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -3.64000
REMARK 3 B22 (A**2) : -3.64000
REMARK 3 B33 (A**2) : 5.46000
REMARK 3 B12 (A**2) : -1.82000
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.402
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.305
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.364
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4497 ; 0.014 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6091 ; 1.871 ; 1.985
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 575 ; 6.445 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 181 ;36.155 ;25.028
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 760 ;19.730 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;20.748 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 701 ; 0.109 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3342 ; 0.008 ; 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): 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 : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 2 A 306
REMARK 3 ORIGIN FOR THE GROUP (A): 5.6619 -27.9739 -9.3727
REMARK 3 T TENSOR
REMARK 3 T11: 0.0059 T22: 0.0952
REMARK 3 T33: 0.0879 T12: -0.0141
REMARK 3 T13: 0.0149 T23: -0.0074
REMARK 3 L TENSOR
REMARK 3 L11: 0.8487 L22: 0.8480
REMARK 3 L33: 0.7556 L12: -0.2365
REMARK 3 L13: 0.0787 L23: 0.6026
REMARK 3 S TENSOR
REMARK 3 S11: -0.0237 S12: 0.0282 S13: -0.1207
REMARK 3 S21: -0.0035 S22: 0.0802 S23: 0.0703
REMARK 3 S31: -0.0003 S32: 0.0026 S33: -0.0565
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 1 B 306
REMARK 3 ORIGIN FOR THE GROUP (A): 32.7133 -35.2272 -4.4591
REMARK 3 T TENSOR
REMARK 3 T11: 0.0711 T22: 0.2165
REMARK 3 T33: 0.1560 T12: -0.0286
REMARK 3 T13: 0.0302 T23: -0.0323
REMARK 3 L TENSOR
REMARK 3 L11: 1.1354 L22: 1.6172
REMARK 3 L33: 1.5455 L12: -0.6053
REMARK 3 L13: 0.0245 L23: 1.2801
REMARK 3 S TENSOR
REMARK 3 S11: -0.0577 S12: 0.1184 S13: 0.2146
REMARK 3 S21: -0.1417 S22: 0.0418 S23: -0.0666
REMARK 3 S31: -0.1868 S32: 0.1052 S33: 0.0159
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 USED IF PRESENT IN
REMARK 3 THE INPUT. U VALUES: WITH TLS ADDED
REMARK 4
REMARK 4 3V4Z 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 RCSB069601.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-AUG-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 19-BM
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : SBC-3
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18282
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700
REMARK 200 RESOLUTION RANGE LOW (A) : 31.600
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 9.900
REMARK 200 R MERGE (I) : 0.09100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 10.10
REMARK 200 R MERGE FOR SHELL (I) : 0.89000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.430
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP, HKL3000
REMARK 200 STARTING MODEL: 1IOW
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.96
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M SODIUM
REMARK 280 CACODYLATE, 50% PEG-200, PH 6.5, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
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 36.76800
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 73.53600
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.53600
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 36.76800
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: 2660 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25020 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 SER A -2
REMARK 465 ASN A -1
REMARK 465 ALA A 0
REMARK 465 MET A 1
REMARK 465 VAL A 208
REMARK 465 PHE A 209
REMARK 465 TYR A 210
REMARK 465 ASP A 211
REMARK 465 TYR A 212
REMARK 465 ASP A 213
REMARK 465 ALA A 214
REMARK 465 LYS A 215
REMARK 465 TYR A 216
REMARK 465 LEU A 217
REMARK 465 SER A 218
REMARK 465 ASP A 219
REMARK 465 SER B -2
REMARK 465 ASN B -1
REMARK 465 ALA B 0
REMARK 465 GLU B 148
REMARK 465 GLY B 149
REMARK 465 SER B 150
REMARK 465 SER B 151
REMARK 465 VAL B 152
REMARK 465 GLY B 207
REMARK 465 VAL B 208
REMARK 465 PHE B 209
REMARK 465 TYR B 210
REMARK 465 ASP B 211
REMARK 465 TYR B 212
REMARK 465 ASP B 213
REMARK 465 ALA B 214
REMARK 465 LYS B 215
REMARK 465 TYR B 216
REMARK 465 LEU B 217
REMARK 465 SER B 218
REMARK 465 ASP B 219
REMARK 465 LYS B 220
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 ARG A 262 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 LEU A 292 CB - CG - CD1 ANGL. DEV. = -10.8 DEGREES
REMARK 500 LEU B 125 CA - CB - CG ANGL. DEV. = 15.2 DEGREES
REMARK 500 ASP B 306 CB - CG - OD2 ANGL. DEV. = 6.0 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 THR A 12 18.35 -144.04
REMARK 500 THR A 48 -35.16 -37.18
REMARK 500 GLU A 52 -30.00 -35.95
REMARK 500 TYR A 114 144.82 -172.12
REMARK 500 PHE A 122 -74.87 -38.66
REMARK 500 GLU A 123 -9.83 -58.12
REMARK 500 GLU A 148 -75.46 -49.40
REMARK 500 SER A 150 -167.52 -77.45
REMARK 500 PRO A 186 -177.70 -68.08
REMARK 500 TRP A 253 167.21 178.04
REMARK 500 GLU A 270 153.49 175.37
REMARK 500 MET A 277 28.96 -143.20
REMARK 500 THR A 278 -150.65 -63.78
REMARK 500 HIS A 280 0.23 -69.17
REMARK 500 ALA A 305 109.97 -51.91
REMARK 500 THR B 42 -7.69 -57.53
REMARK 500 GLN B 204 119.31 -172.09
REMARK 500 PRO B 226 150.15 -45.61
REMARK 500 SER B 230 172.60 -59.79
REMARK 500 LEU B 269 -66.08 -124.75
REMARK 500 ALA B 305 91.85 -65.17
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 PGE B 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 502
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: IDP00575 RELATED DB: TARGETDB
DBREF 3V4Z A 1 306 UNP Q8ZIE7 DDL_YERPE 1 306
DBREF 3V4Z B 1 306 UNP Q8ZIE7 DDL_YERPE 1 306
SEQADV 3V4Z SER A -2 UNP Q8ZIE7 EXPRESSION TAG
SEQADV 3V4Z ASN A -1 UNP Q8ZIE7 EXPRESSION TAG
SEQADV 3V4Z ALA A 0 UNP Q8ZIE7 EXPRESSION TAG
SEQADV 3V4Z SER B -2 UNP Q8ZIE7 EXPRESSION TAG
SEQADV 3V4Z ASN B -1 UNP Q8ZIE7 EXPRESSION TAG
SEQADV 3V4Z ALA B 0 UNP Q8ZIE7 EXPRESSION TAG
SEQRES 1 A 309 SER ASN ALA MET ALA GLU LYS VAL ALA VAL LEU LEU GLY
SEQRES 2 A 309 GLY THR SER ALA GLU ARG GLU VAL SER LEU LEU SER GLY
SEQRES 3 A 309 GLN ALA VAL LEU ALA GLY LEU LYS GLU ALA GLY ILE ASP
SEQRES 4 A 309 ALA TYR GLY VAL ASP THR LYS ASP PHE PRO VAL THR GLN
SEQRES 5 A 309 LEU LYS GLU GLN GLY PHE ASP LYS VAL PHE ILE ALA LEU
SEQRES 6 A 309 HIS GLY ARG GLY GLY GLU ASP GLY THR LEU GLN GLY VAL
SEQRES 7 A 309 LEU GLU PHE LEU GLN LEU PRO TYR THR GLY SER GLY VAL
SEQRES 8 A 309 MET ALA SER ALA LEU THR MET ASP LYS LEU ARG THR LYS
SEQRES 9 A 309 LEU VAL TRP GLN ALA LEU GLY LEU PRO ILE SER PRO TYR
SEQRES 10 A 309 VAL ALA LEU ASN ARG GLN GLN PHE GLU THR LEU SER PRO
SEQRES 11 A 309 GLU GLU LEU VAL ALA CYS VAL ALA LYS LEU GLY LEU PRO
SEQRES 12 A 309 LEU ILE VAL LYS PRO SER HIS GLU GLY SER SER VAL GLY
SEQRES 13 A 309 MET SER LYS VAL ASP HIS ALA SER GLU LEU GLN LYS ALA
SEQRES 14 A 309 LEU VAL GLU ALA PHE GLN HIS ASP SER ASP VAL LEU ILE
SEQRES 15 A 309 GLU LYS TRP LEU SER GLY PRO GLU PHE THR VAL ALA ILE
SEQRES 16 A 309 LEU GLY ASP GLU VAL LEU PRO SER ILE ARG ILE GLN PRO
SEQRES 17 A 309 PRO GLY VAL PHE TYR ASP TYR ASP ALA LYS TYR LEU SER
SEQRES 18 A 309 ASP LYS THR GLN TYR PHE CYS PRO SER GLY LEU SER ASP
SEQRES 19 A 309 GLU SER GLU GLN GLN LEU ALA ALA LEU ALA LEU GLN ALA
SEQRES 20 A 309 TYR HIS ALA LEU ASP CYS SER GLY TRP GLY ARG VAL ASP
SEQRES 21 A 309 VAL MET GLN ASP ARG ASP GLY HIS PHE TYR LEU LEU GLU
SEQRES 22 A 309 VAL ASN THR SER PRO GLY MET THR SER HIS SER LEU VAL
SEQRES 23 A 309 PRO MET ALA ALA ARG GLN TYR GLY LEU SER PHE SER GLN
SEQRES 24 A 309 LEU VAL ALA ARG ILE LEU MET LEU ALA ASP
SEQRES 1 B 309 SER ASN ALA MET ALA GLU LYS VAL ALA VAL LEU LEU GLY
SEQRES 2 B 309 GLY THR SER ALA GLU ARG GLU VAL SER LEU LEU SER GLY
SEQRES 3 B 309 GLN ALA VAL LEU ALA GLY LEU LYS GLU ALA GLY ILE ASP
SEQRES 4 B 309 ALA TYR GLY VAL ASP THR LYS ASP PHE PRO VAL THR GLN
SEQRES 5 B 309 LEU LYS GLU GLN GLY PHE ASP LYS VAL PHE ILE ALA LEU
SEQRES 6 B 309 HIS GLY ARG GLY GLY GLU ASP GLY THR LEU GLN GLY VAL
SEQRES 7 B 309 LEU GLU PHE LEU GLN LEU PRO TYR THR GLY SER GLY VAL
SEQRES 8 B 309 MET ALA SER ALA LEU THR MET ASP LYS LEU ARG THR LYS
SEQRES 9 B 309 LEU VAL TRP GLN ALA LEU GLY LEU PRO ILE SER PRO TYR
SEQRES 10 B 309 VAL ALA LEU ASN ARG GLN GLN PHE GLU THR LEU SER PRO
SEQRES 11 B 309 GLU GLU LEU VAL ALA CYS VAL ALA LYS LEU GLY LEU PRO
SEQRES 12 B 309 LEU ILE VAL LYS PRO SER HIS GLU GLY SER SER VAL GLY
SEQRES 13 B 309 MET SER LYS VAL ASP HIS ALA SER GLU LEU GLN LYS ALA
SEQRES 14 B 309 LEU VAL GLU ALA PHE GLN HIS ASP SER ASP VAL LEU ILE
SEQRES 15 B 309 GLU LYS TRP LEU SER GLY PRO GLU PHE THR VAL ALA ILE
SEQRES 16 B 309 LEU GLY ASP GLU VAL LEU PRO SER ILE ARG ILE GLN PRO
SEQRES 17 B 309 PRO GLY VAL PHE TYR ASP TYR ASP ALA LYS TYR LEU SER
SEQRES 18 B 309 ASP LYS THR GLN TYR PHE CYS PRO SER GLY LEU SER ASP
SEQRES 19 B 309 GLU SER GLU GLN GLN LEU ALA ALA LEU ALA LEU GLN ALA
SEQRES 20 B 309 TYR HIS ALA LEU ASP CYS SER GLY TRP GLY ARG VAL ASP
SEQRES 21 B 309 VAL MET GLN ASP ARG ASP GLY HIS PHE TYR LEU LEU GLU
SEQRES 22 B 309 VAL ASN THR SER PRO GLY MET THR SER HIS SER LEU VAL
SEQRES 23 B 309 PRO MET ALA ALA ARG GLN TYR GLY LEU SER PHE SER GLN
SEQRES 24 B 309 LEU VAL ALA ARG ILE LEU MET LEU ALA ASP
HET PEG A 502 7
HET PGE B 501 10
HETNAM PEG DI(HYDROXYETHYL)ETHER
HETNAM PGE TRIETHYLENE GLYCOL
FORMUL 3 PEG C4 H10 O3
FORMUL 4 PGE C6 H14 O4
FORMUL 5 HOH *23(H2 O)
HELIX 1 1 GLU A 15 GLY A 34 1 20
HELIX 2 2 PRO A 46 LEU A 50 5 5
HELIX 3 3 GLY A 70 GLN A 80 1 11
HELIX 4 4 GLY A 87 MET A 95 1 9
HELIX 5 5 ASP A 96 LEU A 107 1 12
HELIX 6 6 ARG A 119 GLU A 123 1 5
HELIX 7 7 SER A 126 ALA A 135 1 10
HELIX 8 8 LYS A 136 GLY A 138 5 3
HELIX 9 9 HIS A 159 SER A 161 5 3
HELIX 10 10 GLU A 162 GLN A 172 1 11
HELIX 11 11 SER A 230 ALA A 247 1 18
HELIX 12 12 SER A 281 GLY A 291 1 11
HELIX 13 13 SER A 293 LEU A 304 1 12
HELIX 14 14 GLU B 15 ALA B 33 1 19
HELIX 15 15 PRO B 46 LEU B 50 5 5
HELIX 16 16 GLY B 70 GLN B 80 1 11
HELIX 17 17 GLY B 87 THR B 94 1 8
HELIX 18 18 ASP B 96 GLY B 108 1 13
HELIX 19 19 ARG B 119 LEU B 125 1 7
HELIX 20 20 SER B 126 CYS B 133 1 8
HELIX 21 21 VAL B 134 GLY B 138 5 5
HELIX 22 22 GLU B 162 PHE B 171 1 10
HELIX 23 23 SER B 230 LEU B 248 1 19
HELIX 24 24 SER B 281 GLY B 291 1 11
HELIX 25 25 SER B 293 LEU B 304 1 12
SHEET 1 A 3 ALA A 37 ASP A 41 0
SHEET 2 A 3 VAL A 5 LEU A 9 1 N VAL A 5 O TYR A 38
SHEET 3 A 3 LYS A 57 ILE A 60 1 O PHE A 59 N ALA A 6
SHEET 1 B 4 TYR A 114 ASN A 118 0
SHEET 2 B 4 ASP A 176 LYS A 181 -1 O ILE A 179 N VAL A 115
SHEET 3 B 4 LEU A 141 PRO A 145 -1 N LYS A 144 O LEU A 178
SHEET 4 B 4 SER A 155 VAL A 157 -1 O VAL A 157 N LEU A 141
SHEET 1 C 4 GLU A 196 VAL A 197 0
SHEET 2 C 4 GLU A 187 LEU A 193 -1 N LEU A 193 O GLU A 196
SHEET 3 C 4 ILE A 201 GLN A 204 -1 O ILE A 203 N GLU A 187
SHEET 4 C 4 GLN A 222 PHE A 224 -1 O GLN A 222 N GLN A 204
SHEET 1 D 4 GLU A 196 VAL A 197 0
SHEET 2 D 4 GLU A 187 LEU A 193 -1 N LEU A 193 O GLU A 196
SHEET 3 D 4 TRP A 253 GLN A 260 -1 O VAL A 258 N PHE A 188
SHEET 4 D 4 PHE A 266 ASN A 272 -1 O TYR A 267 N MET A 259
SHEET 1 E 3 ALA B 37 ASP B 41 0
SHEET 2 E 3 VAL B 5 LEU B 9 1 N VAL B 7 O VAL B 40
SHEET 3 E 3 LYS B 57 ILE B 60 1 O PHE B 59 N ALA B 6
SHEET 1 F 4 TYR B 114 ASN B 118 0
SHEET 2 F 4 ASP B 176 LYS B 181 -1 O VAL B 177 N LEU B 117
SHEET 3 F 4 LEU B 141 PRO B 145 -1 N LYS B 144 O LEU B 178
SHEET 4 F 4 SER B 155 VAL B 157 -1 O VAL B 157 N LEU B 141
SHEET 1 G 5 GLN B 222 PHE B 224 0
SHEET 2 G 5 GLU B 196 GLN B 204 -1 N ARG B 202 O PHE B 224
SHEET 3 G 5 GLU B 187 LEU B 193 -1 N GLU B 187 O ILE B 203
SHEET 4 G 5 TRP B 253 GLN B 260 -1 O VAL B 258 N PHE B 188
SHEET 5 G 5 PHE B 266 ASN B 272 -1 O GLU B 270 N ASP B 257
CISPEP 1 LEU A 139 PRO A 140 0 0.75
CISPEP 2 GLY A 185 PRO A 186 0 3.13
CISPEP 3 CYS A 225 PRO A 226 0 10.21
CISPEP 4 LEU B 139 PRO B 140 0 -0.02
CISPEP 5 GLY B 185 PRO B 186 0 4.23
CISPEP 6 CYS B 225 PRO B 226 0 0.34
SITE 1 AC1 4 ALA A 25 ALA A 28 PHE A 294 ALA B 25
SITE 1 AC2 4 PRO A 113 LYS A 181 ASP A 261 TYR A 267
CRYST1 100.637 100.637 110.304 90.00 90.00 120.00 P 31 2 1 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 0.009937 0.005737 0.000000 0.00000
SCALE2 0.000000 0.011474 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009066 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
