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 4 20-SEP-23 4HL2 1 REMARK SEQADV LINK 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 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 99.1 REMARK 620 3 HIS A 189 NE2 98.5 123.5 REMARK 620 4 ZZ7 A 301 OXT 173.8 85.6 82.1 REMARK 620 5 HOH A 701 O 90.8 121.4 111.5 83.3 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 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 95.2 REMARK 620 3 HIS A 250 NE2 90.7 110.0 REMARK 620 4 ZZ7 A 301 N3 93.8 130.0 119.0 REMARK 620 5 ZZ7 A 301 O1 168.5 95.2 90.3 75.7 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 GLU A 227 OE2 52.9 REMARK 620 3 GLU B 152 OE2 98.0 81.4 REMARK 620 4 ASP B 223 OD2 106.4 159.3 105.6 REMARK 620 5 HOH B 688 O 117.8 86.6 122.9 104.7 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 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 98.9 REMARK 620 3 HIS B 189 NE2 97.1 124.0 REMARK 620 4 ZZ7 B 302 OXT 173.6 86.3 82.8 REMARK 620 5 HOH B 687 O 91.1 120.5 112.4 83.0 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 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 95.9 REMARK 620 3 HIS B 250 NE2 89.5 110.9 REMARK 620 4 ZZ7 B 302 N3 92.8 135.0 113.3 REMARK 620 5 ZZ7 B 302 O1 167.6 95.5 90.8 75.8 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 NE2 HIS A 120 ZN ZN A 302 1555 1555 2.13 LINK ND1 HIS A 122 ZN ZN A 302 1555 1555 1.98 LINK OD2 ASP A 124 ZN ZN A 303 1555 1555 2.14 LINK NE2 HIS A 189 ZN ZN A 302 1555 1555 2.02 LINK SG CYS A 208 ZN ZN A 303 1555 1555 2.37 LINK OE1AGLU A 227 ZN ZN B 305 1555 1555 2.03 LINK OE2AGLU A 227 ZN ZN B 305 1555 1555 2.69 LINK NE2 HIS A 250 ZN ZN A 303 1555 1555 2.01 LINK OXT ZZ7 A 301 ZN ZN A 302 1555 1555 2.44 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 ZN ZN A 302 O HOH A 701 1555 1555 1.94 LINK NE2 HIS B 120 ZN ZN B 303 1555 1555 2.11 LINK ND1 HIS B 122 ZN ZN B 303 1555 1555 1.96 LINK OD2 ASP B 124 ZN ZN B 304 1555 1555 2.14 LINK OE2 GLU B 152 ZN ZN B 305 1555 1555 2.09 LINK NE2 HIS B 189 ZN ZN B 303 1555 1555 2.00 LINK SG CYS B 208 ZN ZN B 304 1555 1555 2.37 LINK OD2 ASP B 223 ZN ZN B 305 1555 1555 2.07 LINK NE2 HIS B 250 ZN ZN B 304 1555 1555 2.00 LINK OXT ZZ7 B 302 ZN ZN B 303 1555 1555 2.42 LINK N3 ZZ7 B 302 ZN ZN B 304 1555 1555 2.09 LINK O1 ZZ7 B 302 ZN ZN B 304 1555 1555 2.21 LINK ZN ZN B 303 O HOH B 687 1555 1555 1.96 LINK ZN ZN B 305 O HOH B 688 1555 1555 2.05 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