HEADER HYDROLASE 05-MAY-14 4D1W TITLE A H224Y MUTANT FOR VIM-7 FROM PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-B-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METALLO-BETA-LACTAMASE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: STAR KEYWDS HYDROLASE, RESIDUE DETERMINANTS, LIGAND INTERACTION EXPDTA X-RAY DIFFRACTION AUTHOR H.-K.S.LEIROS,S.SKAGSETH,K.S.W.EDVARDSEN,M.S.LORENTZEN,G.E.K.BJERGA, AUTHOR 2 I.LEIROS,O.SAMUELSEN REVDAT 4 20-DEC-23 4D1W 1 REMARK LINK REVDAT 3 17-JAN-18 4D1W 1 REMARK REVDAT 2 13-AUG-14 4D1W 1 JRNL REVDAT 1 25-JUN-14 4D1W 0 JRNL AUTH H.-K.S.LEIROS,S.SKAGSETH,K.S.W.EDVARDSEN,M.S.LORENTZEN, JRNL AUTH 2 G.E.K.BJERGA,I.LEIROS,O.SAMUELSEN JRNL TITL HIS224 ALTERS THE R2 DRUG BINDING SITE AND PHE218 INFLUENCES JRNL TITL 2 THE CATALYTIC EFFICIENCY IN THE METALLO-BETA-LACTAMASE JRNL TITL 3 VIM-7. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 58 4826 2014 JRNL REFN ISSN 0066-4804 JRNL PMID 24913158 JRNL DOI 10.1128/AAC.02735-13 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 41427 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) : 0.120 REMARK 3 R VALUE (WORKING SET) : 0.118 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2196 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2331 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.1240 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.1820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1710 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 258 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.15000 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): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.050 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.302 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1793 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1166 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2445 ; 1.520 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2846 ; 1.101 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 230 ; 6.644 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 73 ;30.635 ;23.699 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 271 ;11.440 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.094 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 289 ; 0.322 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2001 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 351 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 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): 2959 ; 5.495 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 73 ;29.736 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3113 ;11.366 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4D1W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1290060560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43649 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.000 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 2Y8B REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 23.51350 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 35.27025 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 11.75675 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 ASP A 50 OD2 REMARK 480 ASP A 119 OD2 REMARK 480 ASN A 233 ND2 REMARK 480 LYS A 247 CE NZ REMARK 480 GLN A 251 CD OE1 NE2 REMARK 480 LYS A 291 NZ 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 2074 O HOH A 2135 1.72 REMARK 500 OE1 GLN A 251 O HOH A 2239 1.87 REMARK 500 O HOH A 2088 O HOH A 2089 2.03 REMARK 500 O HOH A 2066 O HOH A 2067 2.15 REMARK 500 N ALA A 174 O HOH A 2173 2.15 REMARK 500 O HOH A 2126 O HOH A 2249 2.15 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 NZ LYS A 247 O HOH A 2101 1556 0.12 REMARK 500 CE LYS A 247 O HOH A 2101 1556 1.66 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 LYS A 247 CD LYS A 247 CE 0.210 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 119 CB - CG - OD2 ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG A 248 NE - CZ - NH2 ANGL. DEV. = -3.9 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 ALA A 77 -122.91 52.04 REMARK 500 ASP A 84 143.88 73.04 REMARK 500 TRP A 87 76.75 68.42 REMARK 500 ALA A 195 -105.77 -153.52 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 ASP A 119 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 99.2 REMARK 620 3 HIS A 196 NE2 101.6 111.4 REMARK 620 4 HOH A2118 O 109.3 115.9 116.8 REMARK 620 N 1 2 3 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 OCS A 221 SG 108.2 REMARK 620 3 HIS A 263 NE2 84.8 84.4 REMARK 620 4 HOH A2118 O 85.5 106.8 167.1 REMARK 620 5 HOH A2126 O 93.9 152.7 81.7 90.5 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D1T RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF NATIVE TVIM-7 FROM PSEUDOMONAS REMARK 900 AERUGINOSA REMARK 900 RELATED ID: 4D1U RELATED DB: PDB REMARK 900 A D120A MUTANT OF VIM-7 FROM PSEUDOMONAS AERUGINOSA REMARK 900 RELATED ID: 4D1V RELATED DB: PDB REMARK 900 A F218Y MUTANT OF VIM-7 FROM PSEUDOMONAS AERUGINOSA DBREF 4D1W A 0 300 UNP Q840P9 Q840P9_PSEAI 1 265 SEQADV 4D1W TYR A 224 UNP Q840P9 HIS 200 ENGINEERED MUTATION 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 OCS ALA VAL TYR 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 MODRES 4D1W OCS A 221 CYS CYSTEINESULFONIC ACID HET OCS A 221 9 HET ZN A1293 1 HET ZN A1294 1 HETNAM OCS CYSTEINESULFONIC ACID HETNAM ZN ZINC ION FORMUL 1 OCS C3 H7 N O5 S FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *258(H2 O) HELIX 1 1 GLY A 88 ILE A 104 1 16 HELIX 2 2 HIS A 118 GLY A 123 1 6 HELIX 3 3 GLY A 124 ALA A 131 1 8 HELIX 4 4 SER A 139 GLY A 150 1 12 HELIX 5 5 OCS A 221 VAL A 223 5 3 HELIX 6 6 GLU A 241 TYR A 253 1 13 HELIX 7 7 LEU A 280 LYS A 291 1 12 SHEET 1 AA 7 ARG A 43 GLY A 49 0 SHEET 2 AA 7 VAL A 52 LEU A 61 -1 O VAL A 52 N ILE A 48 SHEET 3 AA 7 THR A 64 ASP A 76 -1 O THR A 64 N LEU A 61 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 C GLY A 220 N OCS A 221 1555 1555 1.32 LINK C OCS A 221 N ALA A 222 1555 1555 1.33 LINK NE2 HIS A 116 ZN ZN A1293 1555 1555 2.07 LINK ND1 HIS A 118 ZN ZN A1293 1555 1555 2.02 LINK OD2 ASP A 120 ZN ZN A1294 1555 1555 2.25 LINK NE2 HIS A 196 ZN ZN A1293 1555 1555 2.00 LINK SG OCS A 221 ZN ZN A1294 1555 1555 2.73 LINK NE2 HIS A 263 ZN ZN A1294 1555 1555 2.23 LINK ZN ZN A1293 O HOH A2118 1555 1555 1.92 LINK ZN ZN A1294 O HOH A2118 1555 1555 2.06 LINK ZN ZN A1294 O HOH A2126 1555 1555 2.26 SITE 1 AC1 7 HIS A 116 HIS A 118 HIS A 196 OCS A 221 SITE 2 AC1 7 ZN A1294 HOH A2118 HOH A2119 SITE 1 AC2 6 ASP A 120 OCS A 221 HIS A 263 ZN A1293 SITE 2 AC2 6 HOH A2118 HOH A2126 CRYST1 70.225 70.225 47.027 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 0.014240 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021264 0.00000