HEADER HYDROLASE/ANTIBIOTIC 10-SEP-14 4RAM TITLE CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 MUTANT M67V TITLE 2 COMPLEXED WITH HYDROLYZED PENICILLIN G COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE NDM-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NDM-1, METALLO-BETA-LACTAMASE NDM-1; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) GOLD; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG50 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, MIDWEST CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, MCSG, STRUCTURES OF MTB PROTEINS CONFERRING SUSCEPTIBILITY KEYWDS 3 TO KNOWN MTB INHIBITORS, MTBI, ALPHA-BETA-BETA-ALPHA SANDWICH, KEYWDS 4 HYDROLASE, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,C.TESAR,R.JEDRZEJCZAK,G.BABNIGG,J.SACCHETTINI,A.JOACHIMIAK, AUTHOR 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG),STRUCTURES OF MTB AUTHOR 3 PROTEINS CONFERRING SUSCEPTIBILITY TO KNOWN MTB INHIBITORS (MTBI) REVDAT 2 20-SEP-23 4RAM 1 REMARK SEQADV LINK REVDAT 1 24-SEP-14 4RAM 0 JRNL AUTH Y.KIM,C.TESAR,R.JEDRZEJCZAK,G.BABNIGG,J.SACCHETTINI, JRNL AUTH 2 A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG), JRNL AUTH 3 STRUCTURES OF MTB PROTEINS CONFERRING SUSCEPTIBILITY TO JRNL AUTH 4 KNOWN MTB INHIBITORS (MTBI) JRNL TITL CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 JRNL TITL 2 MUTANT M67V COMPLEXED WITH HYDROLYZED PENICILLIN G JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1745) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 67087 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3391 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.9780 - 4.3110 0.99 2877 142 0.1676 0.2133 REMARK 3 2 4.3110 - 3.4225 1.00 2809 132 0.1377 0.1566 REMARK 3 3 3.4225 - 2.9901 1.00 2743 133 0.1524 0.1897 REMARK 3 4 2.9901 - 2.7168 1.00 2741 132 0.1566 0.1803 REMARK 3 5 2.7168 - 2.5221 1.00 2704 141 0.1534 0.1809 REMARK 3 6 2.5221 - 2.3734 1.00 2703 146 0.1469 0.1697 REMARK 3 7 2.3734 - 2.2546 1.00 2678 153 0.1401 0.1764 REMARK 3 8 2.2546 - 2.1564 1.00 2664 145 0.1320 0.1630 REMARK 3 9 2.1564 - 2.0734 1.00 2672 151 0.1343 0.1735 REMARK 3 10 2.0734 - 2.0019 1.00 2665 173 0.1332 0.1773 REMARK 3 11 2.0019 - 1.9393 1.00 2611 173 0.1247 0.1610 REMARK 3 12 1.9393 - 1.8839 1.00 2657 135 0.1241 0.1525 REMARK 3 13 1.8839 - 1.8343 1.00 2671 155 0.1237 0.1683 REMARK 3 14 1.8343 - 1.7895 1.00 2656 149 0.1272 0.1592 REMARK 3 15 1.7895 - 1.7488 1.00 2669 157 0.1266 0.2104 REMARK 3 16 1.7488 - 1.7116 1.00 2652 132 0.1374 0.2018 REMARK 3 17 1.7116 - 1.6774 1.00 2659 144 0.1406 0.2000 REMARK 3 18 1.6774 - 1.6457 1.00 2639 127 0.1387 0.1808 REMARK 3 19 1.6457 - 1.6163 1.00 2650 140 0.1336 0.1916 REMARK 3 20 1.6163 - 1.5889 1.00 2674 131 0.1387 0.1847 REMARK 3 21 1.5889 - 1.5633 0.99 2623 120 0.1422 0.2074 REMARK 3 22 1.5633 - 1.5392 0.98 2618 144 0.1436 0.1977 REMARK 3 23 1.5392 - 1.5166 0.94 2475 118 0.1442 0.1820 REMARK 3 24 1.5166 - 1.4952 0.83 2186 118 0.1520 0.2053 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3849 REMARK 3 ANGLE : 1.071 5271 REMARK 3 CHIRALITY : 0.043 586 REMARK 3 PLANARITY : 0.005 708 REMARK 3 DIHEDRAL : 14.895 1366 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4RAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-13 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-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97924 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67683 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 47.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.73800 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: HKL-3000, MOLREP REMARK 200 STARTING MODEL: PDBID 4HL2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6 M SODIUM CHLORIDE, 0.1 M MES PH REMARK 280 6.5, 20 %(W/V) PEG-4000, 5 MM PENICILLIN G, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.53250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.65350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.60600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.65350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.53250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.60600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -278.0 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 28 REMARK 465 ASN A 29 REMARK 465 ALA A 30 REMARK 465 ARG A 270 REMARK 465 SER B 28 REMARK 465 ASN B 29 REMARK 465 ALA B 30 REMARK 465 ARG B 270 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 90 143.35 71.53 REMARK 500 ASP B 90 144.36 72.58 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 A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 99.4 REMARK 620 3 HIS A 189 NE2 103.0 117.5 REMARK 620 4 PNM A 304 O8 177.1 77.9 77.5 REMARK 620 5 HOH A 559 O 97.9 121.4 112.1 84.5 REMARK 620 N 1 2 3 4 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 ASP A 124 OD1 REMARK 620 2 CYS A 208 SG 97.3 REMARK 620 3 HIS A 250 NE2 87.2 112.2 REMARK 620 4 PNM A 304 O12 166.7 95.9 86.8 REMARK 620 5 PNM A 304 N4 98.9 132.7 112.7 72.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 152 OE1 REMARK 620 2 GLU A 152 OE2 53.4 REMARK 620 3 ASP A 223 OD2 97.6 95.7 REMARK 620 4 GLU B 227 OE1 90.8 144.1 91.3 REMARK 620 5 GLU B 227 OE2 82.9 111.3 145.5 54.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 227 OE1 REMARK 620 2 GLU A 227 OE2 52.7 REMARK 620 3 GLU B 152 OE1 89.6 82.1 REMARK 620 4 GLU B 152 OE2 143.1 114.3 53.4 REMARK 620 5 ASP B 223 OD2 95.0 147.4 94.9 88.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 101.0 REMARK 620 3 HIS B 189 NE2 102.3 115.8 REMARK 620 4 HOH B 521 O 101.8 119.2 112.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD1 REMARK 620 2 CYS B 208 SG 96.1 REMARK 620 3 HIS B 250 NE2 90.0 108.9 REMARK 620 4 PNM B 304 O12 168.6 94.6 82.8 REMARK 620 5 PNM B 304 N4 103.9 133.7 112.3 71.0 REMARK 620 6 HOH B 521 O 75.9 81.4 163.6 109.7 64.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 305 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 159 ND1 REMARK 620 2 HOH B 411 O 110.9 REMARK 620 3 HOH B 569 O 99.1 149.6 REMARK 620 N 1 2 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 ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PNM A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PNM B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RKJ RELATED DB: PDB REMARK 900 NDM1, DELTA-38 CONSTRUCT REMARK 900 RELATED ID: 3RKK RELATED DB: PDB REMARK 900 NDM1, DELTA-36NY CONSTRUCT REMARK 900 RELATED ID: 3SBL RELATED DB: PDB REMARK 900 NDM1, DELTA-36NY CONSTRUCT, DIFFERENT CRYSTALS FORM REMARK 900 RELATED ID: 3SFP RELATED DB: PDB REMARK 900 NDM1, DELTA-36NY CONSTRUCT, ONE-ZN-BOUND REMARK 900 RELATED ID: 3SRX RELATED DB: PDB REMARK 900 NDM1, DELTA-36NY CONSTRUCT, TWO-CD-BOUND REMARK 900 RELATED ID: 4GYQ RELATED DB: PDB REMARK 900 NDM1, DELTA-30 CONSTRUCT, D223A MUTANT REMARK 900 RELATED ID: 4H0D RELATED DB: PDB REMARK 900 NDM1, DELTA-30 CONSTRUCT, TWO MN-BOUND AND HYDROLIZED AMPICILLIN REMARK 900 RELATED ID: 4HKY RELATED DB: PDB REMARK 900 NDM1, DELTA-30 CONSTRUCT, TWO CD-BOUND AND PARTIAL FAROPENEM REMARK 900 RELATED ID: 4HL1 RELATED DB: PDB REMARK 900 NDM1, DELTA-30 CONSTRUCT, TWO CD-BOUND AND PARTIAL AMPICILLIN REMARK 900 RELATED ID: 4GYU RELATED DB: PDB REMARK 900 NDM1, DELTA-30 CONSTRUCT, A121F MUTANT REMARK 900 RELATED ID: 4HL2 RELATED DB: PDB REMARK 900 NDM1, DELTA-30 CONSTRUCT, 1.05 A, COMPLEXED WITH HYDROLIZED REMARK 900 AMPICILLIN REMARK 900 RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 4RAW RELATED DB: PDB DBREF 4RAM A 31 270 UNP C7C422 BLAN1_KLEPN 31 270 DBREF 4RAM B 31 270 UNP C7C422 BLAN1_KLEPN 31 270 SEQADV 4RAM SER A 28 UNP C7C422 EXPRESSION TAG SEQADV 4RAM ASN A 29 UNP C7C422 EXPRESSION TAG SEQADV 4RAM ALA A 30 UNP C7C422 EXPRESSION TAG SEQADV 4RAM VAL A 67 UNP C7C422 MET 67 ENGINEERED MUTATION SEQADV 4RAM SER B 28 UNP C7C422 EXPRESSION TAG SEQADV 4RAM ASN B 29 UNP C7C422 EXPRESSION TAG SEQADV 4RAM ALA B 30 UNP C7C422 EXPRESSION TAG SEQADV 4RAM VAL B 67 UNP C7C422 MET 67 ENGINEERED MUTATION SEQRES 1 A 243 SER ASN ALA ILE ARG PRO THR ILE GLY GLN GLN MET GLU SEQRES 2 A 243 THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN SEQRES 3 A 243 LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP SEQRES 4 A 243 VAL PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE SEQRES 5 A 243 VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA SEQRES 6 A 243 TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE SEQRES 7 A 243 LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL SEQRES 8 A 243 THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA SEQRES 9 A 243 LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SEQRES 10 A 243 SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA SEQRES 11 A 243 GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU SEQRES 12 A 243 PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE SEQRES 13 A 243 TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL SEQRES 14 A 243 GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU SEQRES 15 A 243 ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY SEQRES 16 A 243 ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA SEQRES 17 A 243 PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SEQRES 18 A 243 SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS SEQRES 19 A 243 THR ALA ARG MET ALA ASP LYS LEU ARG SEQRES 1 B 243 SER ASN ALA ILE ARG PRO THR ILE GLY GLN GLN MET GLU SEQRES 2 B 243 THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN SEQRES 3 B 243 LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP SEQRES 4 B 243 VAL PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE SEQRES 5 B 243 VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA SEQRES 6 B 243 TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE SEQRES 7 B 243 LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL SEQRES 8 B 243 THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA SEQRES 9 B 243 LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SEQRES 10 B 243 SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA SEQRES 11 B 243 GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU SEQRES 12 B 243 PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE SEQRES 13 B 243 TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL SEQRES 14 B 243 GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU SEQRES 15 B 243 ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY SEQRES 16 B 243 ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA SEQRES 17 B 243 PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SEQRES 18 B 243 SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS SEQRES 19 B 243 THR ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET ZN A 303 1 HET PNM A 304 23 HET CL A 305 1 HET ZN B 301 1 HET ZN B 302 1 HET ZN B 303 1 HET PNM B 304 23 HET ZN B 305 1 HET CL B 306 1 HETNAM ZN ZINC ION HETNAM PNM OPEN FORM - PENICILLIN G HETNAM CL CHLORIDE ION FORMUL 3 ZN 7(ZN 2+) FORMUL 6 PNM 2(C16 H20 N2 O4 S) FORMUL 7 CL 2(CL 1-) FORMUL 14 HOH *370(H2 O) HELIX 1 1 THR A 94 ILE A 109 1 16 HELIX 2 2 HIS A 122 GLY A 127 1 6 HELIX 3 3 GLY A 128 ALA A 135 1 8 HELIX 4 4 ALA A 143 ALA A 149 1 7 HELIX 5 5 PRO A 150 GLY A 153 5 4 HELIX 6 6 GLU A 170 ALA A 174 5 5 HELIX 7 7 HIS A 228 PHE A 240 1 13 HELIX 8 8 ARG A 256 LYS A 268 1 13 HELIX 9 9 THR B 94 ILE B 109 1 16 HELIX 10 10 HIS B 122 GLY B 127 1 6 HELIX 11 11 GLY B 128 ALA B 135 1 8 HELIX 12 12 ALA B 143 ALA B 149 1 7 HELIX 13 13 PRO B 150 GLY B 153 5 4 HELIX 14 14 GLU B 170 ALA B 174 5 5 HELIX 15 15 HIS B 228 PHE B 240 1 13 HELIX 16 16 ARG B 256 LYS B 268 1 13 SHEET 1 A 8 ASP A 43 PHE A 46 0 SHEET 2 A 8 LEU A 49 ALA A 55 -1 O LEU A 49 N PHE A 46 SHEET 3 A 8 VAL A 58 VAL A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 A 8 GLY A 71 ASP A 82 -1 O ILE A 79 N TRP A 59 SHEET 5 A 8 ARG A 85 VAL A 89 -1 O LEU A 87 N VAL A 80 SHEET 6 A 8 VAL A 113 VAL A 117 1 O ALA A 114 N VAL A 86 SHEET 7 A 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 A 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 B 4 LEU A 180 PHE A 183 0 SHEET 2 B 4 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181 SHEET 3 B 4 ILE A 203 PHE A 205 -1 O PHE A 205 N VAL A 196 SHEET 4 B 4 MET A 245 VAL A 247 1 O VAL A 247 N ALA A 204 SHEET 1 C 8 ASP B 43 PHE B 46 0 SHEET 2 C 8 LEU B 49 ALA B 55 -1 O PHE B 51 N GLN B 44 SHEET 3 C 8 VAL B 58 VAL B 67 -1 O GLN B 60 N ARG B 52 SHEET 4 C 8 GLY B 71 ASP B 82 -1 O GLY B 71 N VAL B 67 SHEET 5 C 8 ARG B 85 VAL B 89 -1 O VAL B 89 N LEU B 78 SHEET 6 C 8 VAL B 113 VAL B 117 1 O VAL B 117 N VAL B 88 SHEET 7 C 8 ALA B 138 ASN B 142 1 O TYR B 140 N ALA B 116 SHEET 8 C 8 HIS B 159 LEU B 161 1 O LEU B 161 N ALA B 141 SHEET 1 D 4 LEU B 180 PHE B 183 0 SHEET 2 D 4 THR B 195 ILE B 198 -1 O GLY B 197 N LYS B 181 SHEET 3 D 4 ILE B 203 GLY B 207 -1 O PHE B 205 N VAL B 196 SHEET 4 D 4 MET B 245 MET B 248 1 O VAL B 247 N ALA B 204 LINK NE2 HIS A 120 ZN ZN A 302 1555 1555 2.10 LINK ND1 HIS A 122 ZN ZN A 302 1555 1555 2.01 LINK OD1 ASP A 124 ZN ZN A 301 1555 1555 2.26 LINK OE1 GLU A 152 ZN ZN A 303 1555 1555 2.30 LINK OE2 GLU A 152 ZN ZN A 303 1555 1555 2.54 LINK NE2 HIS A 189 ZN ZN A 302 1555 1555 2.06 LINK SG CYS A 208 ZN ZN A 301 1555 1555 2.40 LINK OD2 ASP A 223 ZN ZN A 303 1555 1555 2.24 LINK OE1 GLU A 227 ZN ZN B 303 1555 1555 2.40 LINK OE2 GLU A 227 ZN ZN B 303 1555 1555 2.51 LINK NE2 HIS A 250 ZN ZN A 301 1555 1555 2.08 LINK ZN ZN A 301 O12 PNM A 304 1555 1555 2.16 LINK ZN ZN A 301 N4 PNM A 304 1555 1555 2.28 LINK ZN ZN A 302 O8 PNM A 304 1555 1555 2.66 LINK ZN ZN A 302 O HOH A 559 1555 1555 1.86 LINK ZN ZN A 303 OE1 GLU B 227 1555 1555 2.37 LINK ZN ZN A 303 OE2 GLU B 227 1555 1555 2.42 LINK NE2 HIS B 120 ZN ZN B 302 1555 1555 2.07 LINK ND1 HIS B 122 ZN ZN B 302 1555 1555 2.02 LINK OD1 ASP B 124 ZN ZN B 301 1555 1555 2.22 LINK OE1 GLU B 152 ZN ZN B 303 1555 1555 2.33 LINK OE2 GLU B 152 ZN ZN B 303 1555 1555 2.51 LINK ND1 HIS B 159 ZN ZN B 305 1555 1555 2.35 LINK NE2 HIS B 189 ZN ZN B 302 1555 1555 2.02 LINK SG CYS B 208 ZN ZN B 301 1555 1555 2.38 LINK OD2 ASP B 223 ZN ZN B 303 1555 1555 2.25 LINK NE2 HIS B 250 ZN ZN B 301 1555 1555 2.08 LINK ZN ZN B 301 O12 PNM B 304 1555 1555 2.14 LINK ZN ZN B 301 N4 PNM B 304 1555 1555 2.40 LINK ZN ZN B 301 O HOH B 521 1555 1555 2.58 LINK ZN ZN B 302 O HOH B 521 1555 1555 1.84 LINK ZN ZN B 305 O HOH B 411 1555 1555 2.62 LINK ZN ZN B 305 O HOH B 569 1555 1555 2.29 SITE 1 AC1 5 ASP A 124 CYS A 208 HIS A 250 PNM A 304 SITE 2 AC1 5 HOH A 559 SITE 1 AC2 5 HIS A 120 HIS A 122 HIS A 189 PNM A 304 SITE 2 AC2 5 HOH A 559 SITE 1 AC3 4 GLU A 152 ASP A 223 CL A 305 GLU B 227 SITE 1 AC4 17 LEU A 65 TRP A 93 HIS A 122 GLN A 123 SITE 2 AC4 17 ASP A 124 HIS A 189 CYS A 208 LYS A 211 SITE 3 AC4 17 GLY A 219 ASN A 220 HIS A 250 ZN A 301 SITE 4 AC4 17 ZN A 302 HOH A 559 THR B 34 GLY B 69 SITE 5 AC4 17 PHE B 70 SITE 1 AC5 3 GLU A 152 ZN A 303 GLU B 227 SITE 1 AC6 5 ASP B 124 CYS B 208 HIS B 250 PNM B 304 SITE 2 AC6 5 HOH B 521 SITE 1 AC7 5 HIS B 120 HIS B 122 HIS B 189 PNM B 304 SITE 2 AC7 5 HOH B 521 SITE 1 AC8 4 GLU A 227 GLU B 152 ASP B 223 CL B 306 SITE 1 AC9 20 THR A 34 PRO A 68 GLY A 69 PHE A 70 SITE 2 AC9 20 LEU B 65 TRP B 93 HIS B 122 GLN B 123 SITE 3 AC9 20 ASP B 124 HIS B 189 CYS B 208 LYS B 211 SITE 4 AC9 20 GLY B 219 ASN B 220 HIS B 250 ZN B 301 SITE 5 AC9 20 ZN B 302 HOH B 401 HOH B 501 HOH B 521 SITE 1 BC1 4 HIS B 159 HOH B 411 HOH B 450 HOH B 569 SITE 1 BC2 4 GLU A 227 GLU B 152 ASP B 223 ZN B 303 CRYST1 39.065 79.212 133.307 90.00 90.00 90.00 P 21 21 21 8 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 0.025598 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012624 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007501 0.00000