HEADER HYDROLASE/ANTIBIOTIC 15-OCT-12 4HL2 TITLE NEW DELHI METALLO-BETA-LACTAMASE-1 1.05 A STRUCTURE COMPLEXED WITH TITLE 2 HYDROLYZED AMPICILLIN 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 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: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 MAGIC; 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, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,C.TESAR,R.JEDRZEJCZAK,J.BABNIGG,J.MIRE,J.SACCHETTINI, AUTHOR 2 A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG), AUTHOR 3 STRUCTURES OF MTB PROTEINS CONFERRING SUSCEPTIBILITY TO KNOWN MTB AUTHOR 4 INHIBITORS (MTBI) REVDAT 3 14-AUG-19 4HL2 1 REMARK REVDAT 2 17-JUL-19 4HL2 1 REMARK REVDAT 1 12-DEC-12 4HL2 0 JRNL AUTH Y.KIM,C.TESAR,R.JEDRZEJCZAK,J.BABNIGG,J.MIRE,J.SACCHETTINI, JRNL AUTH 2 A.JOACHIMIAK JRNL TITL NEW DELHI METALLO-BETA-LACTAMASE-1 1.05 A STRUCTURE JRNL TITL 2 COMPLEXED WITH HYDROLYZED AMPICILLIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1161) 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 184744 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 9286 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 17.5637 - 3.2570 0.92 6057 332 0.1566 0.1839 REMARK 3 2 3.2570 - 2.5878 1.00 6347 340 0.1417 0.1596 REMARK 3 3 2.5878 - 2.2615 1.00 6315 304 0.1332 0.1555 REMARK 3 4 2.2615 - 2.0550 1.00 6263 312 0.1212 0.1403 REMARK 3 5 2.0550 - 1.9079 1.00 6255 352 0.1174 0.1458 REMARK 3 6 1.9079 - 1.7956 1.00 6158 328 0.1181 0.1381 REMARK 3 7 1.7956 - 1.7057 1.00 6190 322 0.1140 0.1265 REMARK 3 8 1.7057 - 1.6315 0.99 6169 296 0.1059 0.1319 REMARK 3 9 1.6315 - 1.5688 0.99 6158 301 0.1055 0.1269 REMARK 3 10 1.5688 - 1.5146 0.98 6091 328 0.1028 0.1348 REMARK 3 11 1.5146 - 1.4673 0.98 6030 320 0.1103 0.1430 REMARK 3 12 1.4673 - 1.4254 0.98 6021 324 0.1088 0.1344 REMARK 3 13 1.4254 - 1.3879 0.96 5896 342 0.1129 0.1495 REMARK 3 14 1.3879 - 1.3540 0.96 5876 336 0.1200 0.1507 REMARK 3 15 1.3540 - 1.3233 0.95 5872 317 0.1262 0.1463 REMARK 3 16 1.3233 - 1.2951 0.94 5806 292 0.1233 0.1445 REMARK 3 17 1.2951 - 1.2692 0.94 5765 312 0.1254 0.1597 REMARK 3 18 1.2692 - 1.2453 0.93 5713 332 0.1307 0.1609 REMARK 3 19 1.2453 - 1.2230 0.93 5718 295 0.1350 0.1678 REMARK 3 20 1.2230 - 1.2023 0.92 5653 290 0.1363 0.1697 REMARK 3 21 1.2023 - 1.1829 0.92 5599 282 0.1421 0.1692 REMARK 3 22 1.1829 - 1.1647 0.91 5610 286 0.1388 0.1743 REMARK 3 23 1.1647 - 1.1476 0.91 5563 296 0.1471 0.1591 REMARK 3 24 1.1476 - 1.1314 0.90 5517 312 0.1507 0.1712 REMARK 3 25 1.1314 - 1.1161 0.90 5517 280 0.1499 0.1609 REMARK 3 26 1.1161 - 1.1017 0.90 5505 318 0.1569 0.1787 REMARK 3 27 1.1017 - 1.0879 0.90 5475 300 0.1705 0.1946 REMARK 3 28 1.0879 - 1.0748 0.89 5513 274 0.1817 0.2035 REMARK 3 29 1.0748 - 1.0623 0.90 5448 275 0.1918 0.2151 REMARK 3 30 1.0623 - 1.0503 0.87 5358 288 0.2106 0.2496 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.80 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 : 0.017 4168 REMARK 3 ANGLE : 1.808 5713 REMARK 3 CHIRALITY : 0.121 623 REMARK 3 PLANARITY : 0.011 779 REMARK 3 DIHEDRAL : 13.824 1527 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 4HL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075599. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-11 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 : 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) : 0.5166 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 : 185255 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 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 (%) : 94.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08900 REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.02300 REMARK 200 FOR SHELL : 0.871 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 3Q6X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULPHATE, 0.1 M BIS REMARK 280 -TRIS PH 5.5, 25 %(W/V) PEG 3350, 100 MM AMPICILLIN, VAPOR REMARK 280 DIFFUSION, 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 19.59500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.23650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.58550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.23650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.58550 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 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 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: 2800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 B 28 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 B 52 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 81 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP B 82 CA - C - N ANGL. DEV. = 12.8 DEGREES REMARK 500 ASP B 82 O - C - N ANGL. DEV. = -11.2 DEGREES REMARK 500 ARG B 85 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 85 NE - CZ - NH2 ANGL. DEV. = -4.1 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 90 143.27 73.55 REMARK 500 PHE B 70 -43.37 -137.22 REMARK 500 ASP B 90 143.29 75.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP B 82 10.14 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 HOH A 701 O REMARK 620 2 HIS A 122 ND1 121.4 REMARK 620 3 HIS A 189 NE2 111.5 123.5 REMARK 620 4 HIS A 120 NE2 90.8 99.1 98.5 REMARK 620 5 ZZ7 A 301 OXT 83.3 85.6 82.1 173.8 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 HOH B 687 O REMARK 620 2 HIS B 122 ND1 120.5 REMARK 620 3 HIS B 189 NE2 112.4 124.0 REMARK 620 4 HIS B 120 NE2 91.1 98.9 97.1 REMARK 620 5 ZZ7 B 302 OXT 83.0 86.3 82.8 173.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 250 NE2 REMARK 620 2 ZZ7 B 302 N3 113.3 REMARK 620 3 ASP B 124 OD2 89.5 92.8 REMARK 620 4 ZZ7 B 302 O1 90.8 75.8 167.6 REMARK 620 5 CYS B 208 SG 110.9 135.0 95.9 95.5 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 HIS A 250 NE2 REMARK 620 2 ASP A 124 OD2 90.7 REMARK 620 3 ZZ7 A 301 N3 119.0 93.8 REMARK 620 4 ZZ7 A 301 O1 90.3 168.5 75.7 REMARK 620 5 CYS A 208 SG 110.0 95.2 130.0 95.2 REMARK 620 N 1 2 3 4 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 GLU A 227 OE1 REMARK 620 2 HOH B 688 O 117.8 REMARK 620 3 ASP B 223 OD2 106.4 104.7 REMARK 620 4 GLU B 152 OE2 98.0 122.9 105.6 REMARK 620 5 GLU A 227 OE2 52.9 86.6 159.3 81.4 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 ZZ7 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 EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZZ7 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 307 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: MCSG-APC105101 RELATED DB: TARGETTRACK DBREF 4HL2 A 31 270 UNP C7C422 BLAN1_KLEPN 31 270 DBREF 4HL2 B 31 270 UNP C7C422 BLAN1_KLEPN 31 270 SEQADV 4HL2 SER A 28 UNP C7C422 EXPRESSION TAG SEQADV 4HL2 ASN A 29 UNP C7C422 EXPRESSION TAG SEQADV 4HL2 ALA A 30 UNP C7C422 EXPRESSION TAG SEQADV 4HL2 SER B 28 UNP C7C422 EXPRESSION TAG SEQADV 4HL2 ASN B 29 UNP C7C422 EXPRESSION TAG SEQADV 4HL2 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 ZZ7 A 301 25 HET ZN A 302 1 HET ZN A 303 1 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO B 301 4 HET ZZ7 B 302 25 HET ZN B 303 1 HET ZN B 304 1 HET ZN B 305 1 HET EDO B 306 4 HET EDO B 307 4 HETNAM ZZ7 (2R,4S)-2-[(R)-{[(2R)-2-AMINO-2- HETNAM 2 ZZ7 PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3- HETNAM 3 ZZ7 THIAZOLIDINE-4-CARBOXYLIC ACID HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN ZZ7 AMPICILLIN (OPEN FORM) HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZZ7 2(C16 H21 N3 O5 S) FORMUL 4 ZN 5(ZN 2+) FORMUL 6 EDO 7(C2 H6 O2) FORMUL 17 HOH *612(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 GLU A 152 5 3 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 MET 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 ARG A 85 N ASP A 82 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 LEU B 49 N PHE B 46 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 ILE B 79 N TRP B 59 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 PHE B 205 -1 O PHE B 205 N VAL B 196 SHEET 4 D 4 MET B 245 VAL B 247 1 O VAL B 247 N ALA B 204 LINK ZN ZN A 302 O HOH A 701 1555 1555 1.94 LINK ZN ZN B 303 O HOH B 687 1555 1555 1.96 LINK ND1 HIS B 122 ZN ZN B 303 1555 1555 1.96 LINK ND1 HIS A 122 ZN ZN A 302 1555 1555 1.98 LINK NE2 HIS B 189 ZN ZN B 303 1555 1555 2.00 LINK NE2 HIS B 250 ZN ZN B 304 1555 1555 2.00 LINK NE2 HIS A 250 ZN ZN A 303 1555 1555 2.01 LINK NE2 HIS A 189 ZN ZN A 302 1555 1555 2.02 LINK OE1AGLU A 227 ZN ZN B 305 1555 1555 2.03 LINK ZN ZN B 305 O HOH B 688 1555 1555 2.05 LINK OD2 ASP B 223 ZN ZN B 305 1555 1555 2.07 LINK N3 ZZ7 B 302 ZN ZN B 304 1555 1555 2.09 LINK OE2 GLU B 152 ZN ZN B 305 1555 1555 2.09 LINK NE2 HIS B 120 ZN ZN B 303 1555 1555 2.11 LINK NE2 HIS A 120 ZN ZN A 302 1555 1555 2.13 LINK OD2 ASP A 124 ZN ZN A 303 1555 1555 2.14 LINK OD2 ASP B 124 ZN ZN B 304 1555 1555 2.14 LINK N3 ZZ7 A 301 ZN ZN A 303 1555 1555 2.18 LINK O1 ZZ7 A 301 ZN ZN A 303 1555 1555 2.20 LINK O1 ZZ7 B 302 ZN ZN B 304 1555 1555 2.21 LINK SG CYS A 208 ZN ZN A 303 1555 1555 2.37 LINK SG CYS B 208 ZN ZN B 304 1555 1555 2.37 LINK OXT ZZ7 B 302 ZN ZN B 303 1555 1555 2.42 LINK OXT ZZ7 A 301 ZN ZN A 302 1555 1555 2.44 LINK OE2AGLU A 227 ZN ZN B 305 1555 1555 2.69 SITE 1 AC1 20 LEU A 65 MET A 67 TRP A 93 HIS A 122 SITE 2 AC1 20 GLN A 123 ASP A 124 HIS A 189 CYS A 208 SITE 3 AC1 20 LYS A 211 GLY A 219 ASN A 220 HIS A 250 SITE 4 AC1 20 ZN A 302 ZN A 303 HOH A 416 HOH A 458 SITE 5 AC1 20 HOH A 701 THR B 34 PRO B 68 GLY B 69 SITE 1 AC2 5 HIS A 120 HIS A 122 HIS A 189 ZZ7 A 301 SITE 2 AC2 5 HOH A 701 SITE 1 AC3 5 ASP A 124 CYS A 208 HIS A 250 ZZ7 A 301 SITE 2 AC3 5 HOH A 701 SITE 1 AC4 4 PRO A 112 VAL A 113 EDO A 305 HOH A 460 SITE 1 AC5 9 ASN A 57 LYS A 106 PRO A 112 GLY A 200 SITE 2 AC5 9 EDO A 304 HOH A 424 HOH A 499 HOH A 560 SITE 3 AC5 9 HOH A 682 SITE 1 AC6 4 ASP A 82 ALA A 134 ALA A 135 HOH A 628 SITE 1 AC7 5 ARG A 234 HOH A 472 HOH A 488 EDO B 306 SITE 2 AC7 5 HOH B 518 SITE 1 AC8 7 ASP A 223 ALA A 224 HOH A 426 ALA B 224 SITE 2 AC8 7 ASP B 225 HOH B 436 HOH B 614 SITE 1 AC9 23 THR A 34 PRO A 68 GLY A 69 LEU B 65 SITE 2 AC9 23 MET B 67 TRP B 93 HIS B 122 GLN B 123 SITE 3 AC9 23 ASP B 124 HIS B 189 CYS B 208 LYS B 211 SITE 4 AC9 23 GLY B 219 ASN B 220 HIS B 250 ZN B 303 SITE 5 AC9 23 ZN B 304 HOH B 410 HOH B 431 HOH B 461 SITE 6 AC9 23 HOH B 589 HOH B 600 HOH B 687 SITE 1 BC1 5 HIS B 120 HIS B 122 HIS B 189 ZZ7 B 302 SITE 2 BC1 5 HOH B 687 SITE 1 BC2 5 ASP B 124 CYS B 208 HIS B 250 ZZ7 B 302 SITE 2 BC2 5 HOH B 687 SITE 1 BC3 4 GLU A 227 GLU B 152 ASP B 223 HOH B 688 SITE 1 BC4 9 ARG A 234 ASP A 267 EDO A 307 HOH A 521 SITE 2 BC4 9 ARG B 234 ALA B 235 ALA B 238 HOH B 427 SITE 3 BC4 9 HOH B 428 SITE 1 BC5 7 GLY A 71 HOH A 503 HOH A 698 ASN B 220 SITE 2 BC5 7 LEU B 221 GLY B 222 HOH B 670 CRYST1 39.190 79.171 134.473 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 0.025517 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007436 0.00000 MASTER 436 0 14 16 24 0 34 6 0 0 0 38 END