HEADER HYDROLASE 12-SEP-14 4RBS TITLE CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 IN THE COMPLEX TITLE 2 WITH HYDROLYZED MEROPENEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE NDM-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 31-270; COMPND 5 SYNONYM: NDM-1, METALLO-BETA-LACTAMASE NDM-1; COMPND 6 EC: 3.5.2.6; COMPND 7 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; 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: PMCSG7 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 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 4RBS 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK REVDAT 1 26-NOV-14 4RBS 0 JRNL AUTH Y.KIM,C.TESAR,R.JEDRZEJCZAK,G.BABNIGG,J.SACCHETTINI, JRNL AUTH 2 A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 IN JRNL TITL 2 THE COMPLEX WITH HYDROLYZED MEROPENEM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.41 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) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 27997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1417 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 41.8406 - 5.1795 1.00 2911 119 0.1692 0.1933 REMARK 3 2 5.1795 - 4.1123 1.00 2737 150 0.1442 0.1755 REMARK 3 3 4.1123 - 3.5928 1.00 2682 158 0.1587 0.1869 REMARK 3 4 3.5928 - 3.2645 1.00 2677 171 0.1696 0.2110 REMARK 3 5 3.2645 - 3.0305 1.00 2668 143 0.1808 0.1964 REMARK 3 6 3.0305 - 2.8519 1.00 2645 133 0.2044 0.2454 REMARK 3 7 2.8519 - 2.7091 1.00 2656 151 0.2075 0.2819 REMARK 3 8 2.7091 - 2.5912 1.00 2618 157 0.2087 0.2506 REMARK 3 9 2.5912 - 2.4915 1.00 2642 123 0.2230 0.2484 REMARK 3 10 2.4915 - 2.4050 0.89 2344 112 0.2375 0.2946 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.60 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 : 0.002 3694 REMARK 3 ANGLE : 0.851 5031 REMARK 3 CHIRALITY : 0.029 561 REMARK 3 PLANARITY : 0.003 669 REMARK 3 DIHEDRAL : 14.583 1299 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 40 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.4995 15.7722 21.8653 REMARK 3 T TENSOR REMARK 3 T11: 0.3869 T22: 0.3752 REMARK 3 T33: 0.4672 T12: -0.1424 REMARK 3 T13: -0.0557 T23: 0.0472 REMARK 3 L TENSOR REMARK 3 L11: 3.0482 L22: 3.8234 REMARK 3 L33: 5.8813 L12: 0.0866 REMARK 3 L13: -1.1419 L23: 0.3201 REMARK 3 S TENSOR REMARK 3 S11: -0.0950 S12: 0.2937 S13: 0.5111 REMARK 3 S21: -0.3894 S22: 0.0563 S23: -0.0458 REMARK 3 S31: -0.4570 S32: 0.0531 S33: 0.0134 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 119 THROUGH 270 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.4871 2.7334 19.2976 REMARK 3 T TENSOR REMARK 3 T11: 0.3582 T22: 0.4407 REMARK 3 T33: 0.3997 T12: -0.1678 REMARK 3 T13: -0.0583 T23: 0.1012 REMARK 3 L TENSOR REMARK 3 L11: 3.2485 L22: 3.4895 REMARK 3 L33: 1.3640 L12: 0.4754 REMARK 3 L13: 0.1963 L23: -0.2111 REMARK 3 S TENSOR REMARK 3 S11: -0.1838 S12: 0.5140 S13: 0.2810 REMARK 3 S21: -0.3454 S22: 0.2761 S23: 0.3213 REMARK 3 S31: -0.0412 S32: -0.1537 S33: -0.0949 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 29 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -44.8441 5.9377 -14.8556 REMARK 3 T TENSOR REMARK 3 T11: 0.6415 T22: 0.2674 REMARK 3 T33: 0.4352 T12: -0.0654 REMARK 3 T13: 0.0194 T23: 0.0536 REMARK 3 L TENSOR REMARK 3 L11: 3.7281 L22: 3.2450 REMARK 3 L33: 4.5164 L12: 0.1908 REMARK 3 L13: 0.9247 L23: -0.8773 REMARK 3 S TENSOR REMARK 3 S11: 0.1732 S12: -0.4218 S13: -0.2918 REMARK 3 S21: 0.6440 S22: 0.0763 S23: 0.3480 REMARK 3 S31: 0.4122 S32: -0.2291 S33: -0.2162 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 119 THROUGH 269 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.5912 21.8288 -14.8913 REMARK 3 T TENSOR REMARK 3 T11: 0.7951 T22: 0.2806 REMARK 3 T33: 0.4086 T12: -0.0705 REMARK 3 T13: 0.1013 T23: 0.0154 REMARK 3 L TENSOR REMARK 3 L11: 2.0741 L22: 3.2310 REMARK 3 L33: 1.3804 L12: 1.2208 REMARK 3 L13: -0.3575 L23: 0.2922 REMARK 3 S TENSOR REMARK 3 S11: 0.2807 S12: -0.2812 S13: 0.1469 REMARK 3 S21: 0.9905 S22: -0.1464 S23: 0.3225 REMARK 3 S31: -0.1185 S32: -0.0409 S33: -0.1257 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 4RBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.97929 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 : 28064 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 16.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56600 REMARK 200 FOR SHELL : 2.210 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: PDB ENTRY 4HL2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8 M SODIUM ACETATE PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 73.32000 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 146.64000 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 146.64000 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 73.32000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: TWO MONOMERS IN THE ASYMMETRIC UNIT 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 SER B 28 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 90 146.69 69.06 REMARK 500 ASP B 90 146.21 72.15 REMARK 500 LYS B 216 19.18 -143.47 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 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 98.7 REMARK 620 3 HIS A 189 NE2 112.6 105.8 REMARK 620 4 0RV A 302 OAF 140.4 87.1 103.1 REMARK 620 N 1 2 3 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 OD2 REMARK 620 2 CYS A 208 SG 90.0 REMARK 620 3 HIS A 250 NE2 90.0 114.7 REMARK 620 4 0RV A 302 NAN 107.1 143.8 97.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 103.2 REMARK 620 3 HIS B 189 NE2 107.5 105.3 REMARK 620 4 0RV B 302 OAF 141.3 92.5 102.0 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 OD2 REMARK 620 2 CYS B 208 SG 97.8 REMARK 620 3 HIS B 250 NE2 98.0 118.0 REMARK 620 4 0RV B 302 NAN 103.4 139.0 93.5 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0RV A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0RV B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY 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 HYDROLYZED REMARK 900 AMPICILLIN REMARK 900 RELATED ID: 4RAM RELATED DB: PDB REMARK 900 NDM1, DELTA-30, M67V MUTANT. COMPLEX WITH PENICILLIN G REMARK 900 RELATED ID: 4RAW RELATED DB: PDB REMARK 900 NDM1, DELTA-30, M67V MUTANT. COMPLEX WITH HYDROLYZED AMPICILLIN REMARK 900 RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK DBREF 4RBS A 31 270 UNP C7C422 BLAN1_KLEPN 31 270 DBREF 4RBS B 31 270 UNP C7C422 BLAN1_KLEPN 31 270 SEQADV 4RBS SER A 28 UNP C7C422 EXPRESSION TAG SEQADV 4RBS ASN A 29 UNP C7C422 EXPRESSION TAG SEQADV 4RBS ALA A 30 UNP C7C422 EXPRESSION TAG SEQADV 4RBS SER B 28 UNP C7C422 EXPRESSION TAG SEQADV 4RBS ASN B 29 UNP C7C422 EXPRESSION TAG SEQADV 4RBS ALA B 30 UNP C7C422 EXPRESSION TAG 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 MET 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 MET 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 300 1 HET ZN A 301 1 HET 0RV A 302 27 HET ACY A 303 4 HET GOL A 304 6 HET GOL A 305 6 HET ZN B 300 1 HET ZN B 301 1 HET 0RV B 302 27 HET ACY B 303 4 HET ACY B 304 4 HET GOL B 305 6 HET ACY B 306 4 HETNAM ZN ZINC ION HETNAM 0RV (2S)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-4-{[(3S,5S)- HETNAM 2 0RV 5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-3- HETNAM 3 0RV METHYL-2H-PYRRO LE-5-CARBOXYLIC ACID HETNAM ACY ACETIC ACID HETNAM GOL GLYCEROL HETSYN 0RV MEROPENEM, HYDROXYLATED FORM HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 4(ZN 2+) FORMUL 5 0RV 2(C17 H25 N3 O6 S) FORMUL 6 ACY 4(C2 H4 O2) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 16 HOH *93(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 GLU A 170 ALA A 174 5 5 HELIX 6 6 HIS A 228 PHE A 240 1 13 HELIX 7 7 ARG A 256 LYS A 268 1 13 HELIX 8 8 ALA B 30 MET B 39 1 10 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 HIS B 228 PHE B 240 1 13 HELIX 14 14 ARG B 256 ASP B 267 1 12 SHEET 1 A 8 GLN A 44 PHE A 46 0 SHEET 2 A 8 LEU A 49 ALA A 55 -1 O PHE A 51 N GLN A 44 SHEET 3 A 8 VAL A 58 MET A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 A 8 GLY A 71 ASP A 82 -1 O GLY A 71 N MET A 67 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 VAL A 117 N VAL A 88 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 THR A 195 N PHE A 183 SHEET 3 B 4 ILE A 203 GLY A 207 -1 O PHE A 205 N VAL A 196 SHEET 4 B 4 MET A 245 MET A 248 1 O VAL A 247 N GLY A 206 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 MET B 67 -1 O GLN B 60 N ARG B 52 SHEET 4 C 8 GLY B 71 ASP B 82 -1 O VAL B 73 N LEU B 65 SHEET 5 C 8 ARG B 85 VAL B 89 -1 O LEU B 87 N VAL B 80 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 5 LEU B 180 PHE B 183 0 SHEET 2 D 5 THR B 195 ILE B 198 -1 O THR B 195 N PHE B 183 SHEET 3 D 5 ILE B 203 GLY B 207 -1 O PHE B 205 N VAL B 196 SHEET 4 D 5 MET B 245 MET B 248 1 O VAL B 247 N GLY B 206 SHEET 5 D 5 SER B 251 ASP B 254 -1 O ASP B 254 N ILE B 246 LINK NE2 HIS A 120 ZN ZN A 300 1555 1555 2.11 LINK ND1 HIS A 122 ZN ZN A 300 1555 1555 1.99 LINK OD2 ASP A 124 ZN ZN A 301 1555 1555 2.22 LINK NE2 HIS A 189 ZN ZN A 300 1555 1555 2.02 LINK SG CYS A 208 ZN ZN A 301 1555 1555 2.34 LINK NE2 HIS A 250 ZN ZN A 301 1555 1555 2.01 LINK ZN ZN A 300 OAF 0RV A 302 1555 1555 1.96 LINK ZN ZN A 301 NAN 0RV A 302 1555 1555 2.14 LINK NE2 HIS B 120 ZN ZN B 300 1555 1555 2.13 LINK ND1 HIS B 122 ZN ZN B 300 1555 1555 1.98 LINK OD2 ASP B 124 ZN ZN B 301 1555 1555 2.13 LINK NE2 HIS B 189 ZN ZN B 300 1555 1555 2.01 LINK SG CYS B 208 ZN ZN B 301 1555 1555 2.27 LINK NE2 HIS B 250 ZN ZN B 301 1555 1555 1.99 LINK ZN ZN B 300 OAF 0RV B 302 1555 1555 2.15 LINK ZN ZN B 301 NAN 0RV B 302 1555 1555 2.15 SITE 1 AC1 4 HIS A 120 HIS A 122 HIS A 189 0RV A 302 SITE 1 AC2 4 ASP A 124 CYS A 208 HIS A 250 0RV A 302 SITE 1 AC3 13 TRP A 93 HIS A 122 ASP A 124 HIS A 189 SITE 2 AC3 13 CYS A 208 LYS A 211 GLY A 219 ASN A 220 SITE 3 AC3 13 HIS A 250 ZN A 300 ZN A 301 GLY B 69 SITE 4 AC3 13 0RV B 302 SITE 1 AC4 3 PRO A 112 VAL A 113 HOH A 448 SITE 1 AC5 6 ASN A 166 TRP A 168 PHE A 183 ALA A 235 SITE 2 AC5 6 ALA A 238 ALA A 239 SITE 1 AC6 3 ARG A 256 ILE A 259 THR A 260 SITE 1 AC7 4 HIS B 120 HIS B 122 HIS B 189 0RV B 302 SITE 1 AC8 4 ASP B 124 CYS B 208 HIS B 250 0RV B 302 SITE 1 AC9 14 GLY A 69 PHE A 70 0RV A 302 HIS B 122 SITE 2 AC9 14 GLN B 123 ASP B 124 HIS B 189 CYS B 208 SITE 3 AC9 14 LYS B 211 GLY B 219 ASN B 220 HIS B 250 SITE 4 AC9 14 ZN B 300 ZN B 301 SITE 1 BC1 4 ARG B 85 ALA B 114 ASN B 176 HOH B 432 SITE 1 BC2 3 PRO B 112 VAL B 113 ALA B 135 SITE 1 BC3 6 ASN B 166 TRP B 168 PHE B 183 ALA B 235 SITE 2 BC3 6 ALA B 238 ALA B 239 SITE 1 BC4 5 ASN B 57 ARG B 81 ILE B 198 THR B 201 SITE 2 BC4 5 HOH B 422 CRYST1 74.428 74.428 219.960 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 0.013436 0.007757 0.000000 0.00000 SCALE2 0.000000 0.015514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004546 0.00000