HEADER HYDROLASE 03-FEB-11 2Y87 TITLE NATIVE VIM-7. STRUCTURAL AND COMPUTATIONAL INVESTIGATIONS OF VIM-7: TITLE 2 INSIGHTS INTO THE SUBSTRATE SPECIFICITY OF VIM METALLO-BETA- TITLE 3 LACTAMASES COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-B-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METALLO-BETA-LACTAMASE VIM-7, METALLO-BETA-LACTAMASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE, CEPHALOSPORINS, ANTIBIOTIC RECOGNITION EXPDTA X-RAY DIFFRACTION AUTHOR P.SARADHI,H.-K.S.LEIROS,R.AHMAD,J.SPENCER,I.LEIROS,T.R.WALSH, AUTHOR 2 A.SUNDSFJORD,O.SAMUELSEN REVDAT 3 20-DEC-23 2Y87 1 REMARK LINK REVDAT 2 31-AUG-11 2Y87 1 JRNL REMARK VERSN REVDAT 1 15-JUN-11 2Y87 0 JRNL AUTH P.SARADHI,H.-K.S.LEIROS,R.AHMAD,J.SPENCER,I.LEIROS, JRNL AUTH 2 T.R.WALSH,A.SUNDSFJORD,O.SAMUELSEN JRNL TITL STRUCTURAL AND COMPUTATIONAL INVESTIGATIONS OF VIM- 7: JRNL TITL 2 INSIGHTS INTO THE SUBSTRATE SPECIFICITY OF VIM JRNL TITL 3 METALLO-BETA-LACTAMASES JRNL REF J.MOL.BIOL. V. 411 174 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21645522 JRNL DOI 10.1016/J.JMB.2011.05.035 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 17386 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1984 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 915 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1705 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.07000 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): 0.136 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.606 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1734 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2356 ; 1.685 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 219 ; 6.784 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 73 ;35.088 ;23.973 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 260 ;12.804 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;16.306 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1293 ; 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): 1121 ; 0.990 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1791 ; 1.702 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 613 ; 2.782 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 565 ; 4.721 ; 4.500 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 : 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. REMARK 4 REMARK 4 2Y87 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1290047266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.240 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19415 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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: PDB ENTRY 1KO3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22.5-23.5% POLYETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHERS (PEG MME) 2K, 0.1 M CALCIUM ACETATE, 0.1 M REMARK 280 SODIUM CACODYLATE PH 5.0, 8 MM BETA-MERCAPTOETHANOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.78100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.67150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.89050 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 0 REMARK 465 PHE A 1 REMARK 465 GLN A 2 REMARK 465 ILE A 3 REMARK 465 ARG A 4 REMARK 465 SER A 5 REMARK 465 PHE A 6 REMARK 465 LEU A 7 REMARK 465 VAL A 8 REMARK 465 GLY A 9 REMARK 465 ILE A 10 REMARK 465 SER A 11 REMARK 465 ALA A 12 REMARK 465 PHE A 13 REMARK 465 VAL A 14 REMARK 465 MET A 15 REMARK 465 ALA A 16 REMARK 465 VAL A 17 REMARK 465 LEU A 18 REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 ALA A 21 REMARK 465 ALA A 22 REMARK 465 TYR A 23 REMARK 465 SER A 24 REMARK 465 ALA A 25 REMARK 465 GLN A 26 REMARK 465 PRO A 27 REMARK 465 GLY A 28 REMARK 465 GLY A 29 REMARK 465 HIS A 293 REMARK 465 LYS A 294 REMARK 465 VAL A 295 REMARK 465 ARG A 296 REMARK 465 PRO A 297 REMARK 465 VAL A 298 REMARK 465 ALA A 299 REMARK 465 GLU A 300 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 247 CD CE NZ REMARK 480 LYS A 291 CD CE NZ REMARK 480 THR A 292 OG1 CG2 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 O HOH A 2066 O HOH A 2095 2.17 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 TYR A 45 C LYS A 47 N 0.214 REMARK 500 PRO A 107 C VAL A 109 N 0.158 REMARK 500 ALA A 131 C GLY A 133 N 0.187 REMARK 500 GLY A 150 C ASN A 165 N 0.308 REMARK 500 VAL A 205 C PRO A 209 N 0.191 REMARK 500 VAL A 211 C ARG A 215 N 0.168 REMARK 500 LEU A 265 C PRO A 277 N 0.145 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 PRO A 107 O - C - N ANGL. DEV. = -11.6 DEGREES REMARK 500 ALA A 131 CA - C - N ANGL. DEV. = 13.3 DEGREES REMARK 500 ALA A 131 O - C - N ANGL. DEV. = -14.6 DEGREES REMARK 500 GLY A 150 O - C - N ANGL. DEV. = -21.1 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 LEU A 61 -63.33 -107.68 REMARK 500 ALA A 77 -117.60 56.83 REMARK 500 ASP A 84 146.20 73.88 REMARK 500 TRP A 87 67.64 68.65 REMARK 500 ALA A 174 26.03 -74.13 REMARK 500 ALA A 195 -103.74 -158.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 62 ASP A 63 144.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 150 27.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 MICROHETEROGENEITY OBSERVED BETWEEN SULPHUR OF UNX A1296 AND REMARK 600 HOH A2000. REMARK 600 THE AUTHOR SUGGESTS THE IDENTITY OF THE UNX ION IS SULPHUR 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 ZN A1293 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 116 NE2 REMARK 620 2 HIS A 118 ND1 101.7 REMARK 620 3 HIS A 196 NE2 100.2 107.3 REMARK 620 4 UNX A1296 UNK 132.6 109.2 103.7 REMARK 620 5 HOH A2000 O 128.6 116.6 99.5 7.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1295 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 119 OD2 REMARK 620 2 ASP A 119 OD1 50.7 REMARK 620 3 ASN A 165 OD1 119.8 78.5 REMARK 620 4 HOH A2066 O 83.6 75.0 115.7 REMARK 620 5 HOH A2093 O 149.3 146.5 68.1 121.5 REMARK 620 6 HOH A2095 O 147.0 119.3 81.4 63.8 59.2 REMARK 620 7 HOH A2097 O 84.1 102.7 77.2 165.6 68.2 127.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1294 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 120 OD2 REMARK 620 2 CYS A 221 SG 106.5 REMARK 620 3 HIS A 263 NE2 87.7 104.1 REMARK 620 4 UNX A1296 UNK 103.4 132.1 113.8 REMARK 620 5 HOH A2000 O 108.6 119.4 124.8 12.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1295 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y8A RELATED DB: PDB REMARK 900 VIM-7 WITH OXIDISED. STRUCTURAL AND COMPUTATIONAL INVESTIGATIONS OF REMARK 900 VIM-7: INSIGHTS INTO THE SUBSTRATE SPECIFICITY OF VIM METALLO-BETA- REMARK 900 LACTAMASES REMARK 900 RELATED ID: 2Y8B RELATED DB: PDB REMARK 900 VIM-7 WITH OXIDISED. STRUCTURAL AND COMPUTATIONAL INVESTIGATIONS OF REMARK 900 VIM-7: INSIGHTS INTO THE SUBSTRATE SPECIFICITY OF VIM METALLO-BETA- REMARK 900 LACTAMASES REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHOR DEFINED DISCONTINUOUS RESIDUE NUMBERING. THE SEQUENCE REMARK 999 IS NUMBERED ACCORDING TO THE BBL NUMBERING SCHEME (REFERENCE REMARK 999 GARAU, G. ET AL (2004). UPDATE OF THE STANDARD NUMBERING REMARK 999 SCHEME FOR CLASS B B -LACTAMASES. ANTIMICROB. AGENTS REMARK 999 CHEMOTHER. 48, 2347-9.) HENCE GIVING INCONSECUTIVE NUMBERING REMARK 999 OF RESIDUES. DBREF 2Y87 A 0 300 UNP Q840P9 Q840P9_PSEAE 1 265 SEQRES 1 A 265 MET PHE GLN ILE ARG SER PHE LEU VAL GLY ILE SER ALA SEQRES 2 A 265 PHE VAL MET ALA VAL LEU GLY SER ALA ALA TYR SER ALA SEQRES 3 A 265 GLN PRO GLY GLY GLU TYR PRO THR VAL ASP ASP ILE PRO SEQRES 4 A 265 VAL GLY GLU VAL ARG LEU TYR LYS ILE GLY ASP GLY VAL SEQRES 5 A 265 TRP SER HIS ILE ALA THR GLN LYS LEU GLY ASP THR VAL SEQRES 6 A 265 TYR SER SER ASN GLY LEU ILE VAL ARG ASP ALA ASP GLU SEQRES 7 A 265 LEU LEU LEU ILE ASP THR ALA TRP GLY ALA LYS ASN THR SEQRES 8 A 265 VAL ALA LEU LEU ALA GLU ILE GLU LYS GLN ILE GLY LEU SEQRES 9 A 265 PRO VAL THR ARG SER ILE SER THR HIS PHE HIS ASP ASP SEQRES 10 A 265 ARG VAL GLY GLY VAL ASP VAL LEU ARG ALA ALA GLY VAL SEQRES 11 A 265 ALA THR TYR THR SER PRO LEU THR ARG GLN LEU ALA GLU SEQRES 12 A 265 ALA ALA GLY ASN GLU VAL PRO ALA HIS SER LEU LYS ALA SEQRES 13 A 265 LEU SER SER SER GLY ASP VAL VAL ARG PHE GLY PRO VAL SEQRES 14 A 265 GLU VAL PHE TYR PRO GLY ALA ALA HIS SER GLY ASP ASN SEQRES 15 A 265 LEU VAL VAL TYR VAL PRO ALA VAL ARG VAL LEU PHE GLY SEQRES 16 A 265 GLY CYS ALA VAL HIS GLU ALA SER ARG GLU SER ALA GLY SEQRES 17 A 265 ASN VAL ALA ASP ALA ASN LEU ALA GLU TRP PRO ALA THR SEQRES 18 A 265 ILE LYS ARG ILE GLN GLN ARG TYR PRO GLU ALA GLU VAL SEQRES 19 A 265 VAL ILE PRO GLY HIS GLY LEU PRO GLY GLY LEU GLU LEU SEQRES 20 A 265 LEU GLN HIS THR THR ASN VAL VAL LYS THR HIS LYS VAL SEQRES 21 A 265 ARG PRO VAL ALA GLU HET ZN A1293 1 HET ZN A1294 1 HET MG A1295 1 HET UNX A1296 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 MG MG 2+ FORMUL 5 UNX X FORMUL 6 HOH *170(H2 O) HELIX 1 1 THR A 33 ILE A 37 5 5 HELIX 2 2 GLY A 88 ILE A 104 1 16 HELIX 3 3 HIS A 118 GLY A 123 1 6 HELIX 4 4 GLY A 124 ALA A 131 1 8 HELIX 5 5 SER A 139 ALA A 149 1 11 HELIX 6 6 CYS A 221 VAL A 223 5 3 HELIX 7 7 GLU A 241 TYR A 253 1 13 HELIX 8 8 LEU A 280 THR A 292 1 13 SHEET 1 AA 7 ARG A 43 GLY A 49 0 SHEET 2 AA 7 VAL A 52 LYS A 60 -1 O VAL A 52 N ILE A 48 SHEET 3 AA 7 VAL A 66 ASP A 76 -1 O TYR A 67 N GLN A 59 SHEET 4 AA 7 GLU A 79 ILE A 83 -1 O GLU A 79 N ASP A 76 SHEET 5 AA 7 VAL A 109 ILE A 113 1 N THR A 110 O LEU A 80 SHEET 6 AA 7 ALA A 135 THR A 138 1 O ALA A 135 N SER A 112 SHEET 7 AA 7 HIS A 170 SER A 171 1 O HIS A 170 N THR A 138 SHEET 1 AB 5 ASP A 180 PHE A 184 0 SHEET 2 AB 5 VAL A 187 TYR A 191 -1 O VAL A 187 N PHE A 184 SHEET 3 AB 5 VAL A 202 VAL A 205 -1 O VAL A 202 N PHE A 190 SHEET 4 AB 5 VAL A 216 GLY A 220 -1 O VAL A 216 N VAL A 205 SHEET 5 AB 5 VAL A 258 PRO A 261 1 O VAL A 258 N LEU A 217 LINK NE2 HIS A 116 ZN ZN A1293 1555 1555 2.06 LINK ND1 HIS A 118 ZN ZN A1293 1555 1555 2.04 LINK OD2 ASP A 119 MG MG A1295 1555 1555 2.46 LINK OD1 ASP A 119 MG MG A1295 1555 1555 2.61 LINK OD2 ASP A 120 ZN ZN A1294 1555 1555 2.04 LINK OD1 ASN A 165 MG MG A1295 1555 1555 2.41 LINK NE2 HIS A 196 ZN ZN A1293 1555 1555 2.11 LINK SG CYS A 221 ZN ZN A1294 1555 1555 2.32 LINK NE2 HIS A 263 ZN ZN A1294 1555 1555 2.13 LINK ZN ZN A1293 UNKBUNX A1296 1555 1555 2.50 LINK ZN ZN A1293 O AHOH A2000 1555 1555 2.05 LINK ZN ZN A1294 UNKBUNX A1296 1555 1555 2.41 LINK ZN ZN A1294 O AHOH A2000 1555 1555 2.30 LINK MG MG A1295 O HOH A2066 1555 1555 1.77 LINK MG MG A1295 O HOH A2093 1555 1555 2.66 LINK MG MG A1295 O HOH A2095 1555 1555 2.27 LINK MG MG A1295 O HOH A2097 1555 1555 2.00 SITE 1 AC1 5 HIS A 116 HIS A 118 HIS A 196 ZN A1294 SITE 2 AC1 5 HOH A2000 SITE 1 AC2 5 ASP A 120 CYS A 221 HIS A 263 ZN A1293 SITE 2 AC2 5 HOH A2000 SITE 1 AC3 6 ASP A 119 ASN A 165 HOH A2066 HOH A2093 SITE 2 AC3 6 HOH A2095 HOH A2097 CRYST1 70.399 70.399 47.562 90.00 90.00 90.00 P 43 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 0.014205 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021025 0.00000