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 3 13-SEP-23 3V4Z 1 REMARK SEQADV REVDAT 2 08-NOV-17 3V4Z 1 REMARK 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 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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) : 2.70 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER 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 DEPOSITION ID IS D_1000069601. 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 : DENZO, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, 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 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 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, HKL-3000 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