HEADER HYDROLASE 20-MAR-18 5ZJC TITLE CRYSTAL STRUCTURE OF NDM-1 IN COMPLEX WITH D-CAPTOPRIL DERIVATIVE CY41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE TYPE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: B2 METALLO-BETA-LACTAMASE,BETA-LACTAMASE TYPE II,METALLO- COMPND 5 BETA-LACTAMASE NDM-1,METALLO-BETA-LACTAMASE TYPE II,NEW DELHI COMPND 6 METALLO-BETA-LACTAMASE-1,NDM-1; COMPND 7 EC: 3.5.2.6; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLANDM-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRHISMBP KEYWDS NDM-1, METALLO-BETA-LACTAMASE, ANTIBIOTIC RESISTENT, INHIBITOR, THIO KEYWDS 2 COMPOUNDS, ANTIBIOTIC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,Q.HAO REVDAT 2 22-NOV-23 5ZJC 1 REMARK REVDAT 1 20-MAR-19 5ZJC 0 JRNL AUTH H.ZHANG,Q.HAO JRNL TITL CRYSTAL STRUCTURE OF NDM-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 3 NUMBER OF REFLECTIONS : 100828 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5330 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) : 0.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 941 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 10.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1697 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 0.54000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.41000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.021 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.022 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.014 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.600 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.981 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1837 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1685 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2509 ; 1.376 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3918 ; 0.984 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 250 ; 6.526 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;31.213 ;24.615 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 288 ;12.010 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;18.480 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 277 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2125 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 367 ; 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): 3522 ; 1.064 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 195 ;17.167 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3575 ; 4.907 ; 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 : 4 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 43 A 70 REMARK 3 ORIGIN FOR THE GROUP (A): -2.5773 -6.6739 -1.7239 REMARK 3 T TENSOR REMARK 3 T11: 0.0506 T22: 0.0884 REMARK 3 T33: 0.0271 T12: -0.0116 REMARK 3 T13: 0.0261 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 1.1662 L22: 3.6888 REMARK 3 L33: 0.6816 L12: 0.5820 REMARK 3 L13: -0.2014 L23: 0.3611 REMARK 3 S TENSOR REMARK 3 S11: 0.0134 S12: -0.0935 S13: 0.1103 REMARK 3 S21: 0.0591 S22: -0.0244 S23: 0.1269 REMARK 3 S31: -0.0469 S32: -0.0027 S33: 0.0110 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 : A 71 A 169 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0007 -14.3155 -11.9292 REMARK 3 T TENSOR REMARK 3 T11: 0.0258 T22: 0.0586 REMARK 3 T33: 0.0161 T12: 0.0024 REMARK 3 T13: 0.0187 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.3040 L22: 1.1264 REMARK 3 L33: 0.6755 L12: 0.0817 REMARK 3 L13: -0.0914 L23: 0.0946 REMARK 3 S TENSOR REMARK 3 S11: 0.0053 S12: -0.0350 S13: -0.0165 REMARK 3 S21: -0.0483 S22: -0.0364 S23: -0.0165 REMARK 3 S31: 0.0072 S32: 0.0341 S33: 0.0310 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 170 A 241 REMARK 3 ORIGIN FOR THE GROUP (A): -11.4640 -13.8394 -16.9961 REMARK 3 T TENSOR REMARK 3 T11: 0.0231 T22: 0.0635 REMARK 3 T33: 0.0469 T12: -0.0018 REMARK 3 T13: -0.0122 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.0371 L22: 0.9478 REMARK 3 L33: 0.7091 L12: -0.3526 REMARK 3 L13: -0.1785 L23: -0.0289 REMARK 3 S TENSOR REMARK 3 S11: -0.0205 S12: 0.0236 S13: 0.0401 REMARK 3 S21: -0.0753 S22: 0.0033 S23: 0.1635 REMARK 3 S31: -0.0007 S32: -0.0857 S33: 0.0172 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 242 A 270 REMARK 3 ORIGIN FOR THE GROUP (A): -18.5873 -8.6176 -13.0791 REMARK 3 T TENSOR REMARK 3 T11: 0.0138 T22: 0.0978 REMARK 3 T33: 0.0701 T12: -0.0001 REMARK 3 T13: 0.0103 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 2.3510 L22: 0.9050 REMARK 3 L33: 1.5296 L12: 0.0225 REMARK 3 L13: 0.2618 L23: 0.5081 REMARK 3 S TENSOR REMARK 3 S11: -0.0354 S12: 0.1418 S13: 0.1088 REMARK 3 S21: -0.0604 S22: 0.0650 S23: 0.1087 REMARK 3 S31: -0.0791 S32: -0.1556 S33: -0.0295 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5ZJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300007169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119689 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.960 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3Q6X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH5.5, 15% PEG 3350, REMARK 280 20MM L-PROLINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 29.99000 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: MONOMERIC 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 GLY A 29 REMARK 465 GLU A 30 REMARK 465 ILE A 31 REMARK 465 ARG A 32 REMARK 465 PRO A 33 REMARK 465 THR A 34 REMARK 465 ILE A 35 REMARK 465 GLY A 36 REMARK 465 GLN A 37 REMARK 465 GLN A 38 REMARK 465 MET A 39 REMARK 465 GLU A 40 REMARK 465 THR A 41 REMARK 465 GLY A 42 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 85 NE - CZ - NH2 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 ASP A 90 141.29 76.84 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 694 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 695 DISTANCE = 6.00 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 98.5 REMARK 620 3 HIS A 189 NE2 99.5 114.4 REMARK 620 4 9EX A 305 S1 136.0 110.4 97.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 109.5 REMARK 620 3 HIS A 250 NE2 93.7 104.7 REMARK 620 4 9EX A 305 S1 115.5 113.0 118.5 REMARK 620 N 1 2 3 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9EX A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ZIO RELATED DB: PDB REMARK 900 NDM-1 IN COMPLEX WITH L-CAPTOPRIL REMARK 900 RELATED ID: 5ZJ2 RELATED DB: PDB REMARK 900 NDM-1 IN COMPLEX WITH D-CAPTOPRIL REMARK 900 RELATED ID: 5ZJ1 RELATED DB: PDB REMARK 900 NDM-1 IN COMPLEX WITH D-CAPTOPRIL DERIVATIVE CYT-14 REMARK 900 RELATED ID: 5ZJ7 RELATED DB: PDB REMARK 900 NDM-1 IN COMPLEX WITH D-CAPTOPRIL DERIVATIVE CY22 REMARK 900 RELATED ID: 5ZJ8 RELATED DB: PDB REMARK 900 NDM-1 IN COMPLEX WITH D-CAPTOPRIL DERIVATIVE CY32 DBREF 5ZJC A 29 270 UNP C7C422 BLAN1_KLEPN 29 270 SEQRES 1 A 242 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR SEQRES 2 A 242 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU SEQRES 3 A 242 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET SEQRES 4 A 242 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL SEQRES 5 A 242 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP SEQRES 6 A 242 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS SEQRES 7 A 242 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR SEQRES 8 A 242 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU SEQRES 9 A 242 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER SEQRES 10 A 242 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN SEQRES 11 A 242 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO SEQRES 12 A 242 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR SEQRES 13 A 242 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY SEQRES 14 A 242 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE SEQRES 15 A 242 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP SEQRES 16 A 242 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE SEQRES 17 A 242 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER SEQRES 18 A 242 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR SEQRES 19 A 242 ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET EDO A 303 4 HET EDO A 304 4 HET 9EX A 305 6 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM 9EX (2S)-2-METHYL-3-SULFANYL-PROPAN-1-OL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 9EX C4 H10 O S FORMUL 7 HOH *295(H2 O) HELIX 1 AA1 THR A 94 ILE A 109 1 16 HELIX 2 AA2 HIS A 122 GLY A 127 1 6 HELIX 3 AA3 GLY A 128 ALA A 135 1 8 HELIX 4 AA4 ALA A 143 GLY A 153 1 11 HELIX 5 AA5 GLU A 170 ALA A 174 5 5 HELIX 6 AA6 GLY A 207 ILE A 210 5 4 HELIX 7 AA7 HIS A 228 PHE A 240 1 13 HELIX 8 AA8 ARG A 256 LYS A 268 1 13 SHEET 1 AA1 8 GLN A 44 PHE A 46 0 SHEET 2 AA1 8 LEU A 49 ALA A 55 -1 O LEU A 49 N PHE A 46 SHEET 3 AA1 8 VAL A 58 MET A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 AA1 8 GLY A 71 ASP A 82 -1 O GLY A 71 N MET A 67 SHEET 5 AA1 8 ARG A 85 VAL A 89 -1 O LEU A 87 N VAL A 80 SHEET 6 AA1 8 VAL A 113 VAL A 118 1 O VAL A 117 N VAL A 88 SHEET 7 AA1 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 AA1 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 AA2 4 LEU A 180 PHE A 183 0 SHEET 2 AA2 4 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181 SHEET 3 AA2 4 ILE A 203 PHE A 205 -1 O PHE A 205 N VAL A 196 SHEET 4 AA2 4 MET A 245 VAL A 247 1 O VAL A 247 N ALA A 204 LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 2.07 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 2.05 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 1.93 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 2.06 LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.31 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 2.03 LINK ZN ZN A 301 S1 9EX A 305 1555 1555 2.30 LINK ZN ZN A 302 S1 9EX A 305 1555 1555 2.29 SITE 1 AC1 5 HIS A 120 HIS A 122 HIS A 189 ZN A 302 SITE 2 AC1 5 9EX A 305 SITE 1 AC2 5 ASP A 124 CYS A 208 HIS A 250 ZN A 301 SITE 2 AC2 5 9EX A 305 SITE 1 AC3 5 ALA A 121 LEU A 148 GLU A 152 THR A 190 SITE 2 AC3 5 ASP A 192 SITE 1 AC4 8 HIS A 133 GLY A 237 ARG A 256 ILE A 259 SITE 2 AC4 8 HOH A 429 HOH A 499 HOH A 510 HOH A 567 SITE 1 AC5 10 MET A 67 TRP A 93 HIS A 122 ASP A 124 SITE 2 AC5 10 HIS A 189 ASN A 220 HIS A 250 ZN A 301 SITE 3 AC5 10 ZN A 302 HOH A 405 CRYST1 41.610 59.980 42.067 90.00 97.88 90.00 P 1 21 1 2 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 0.024033 0.000000 0.003327 0.00000 SCALE2 0.000000 0.016672 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023998 0.00000