HEADER HYDROLASE/ANTIBIOTIC 11-SEP-14 4RAW TITLE CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 MUTANT M67V TITLE 2 COMPLEXED WITH 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; 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 4RAW 1 REMARK SEQADV LINK REVDAT 1 26-NOV-14 4RAW 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 AMPICILLIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 98492 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 4910 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 29.4161 - 4.0412 0.99 3501 170 0.1460 0.1598 REMARK 3 2 4.0412 - 3.2089 1.00 3384 147 0.1370 0.1743 REMARK 3 3 3.2089 - 2.8037 1.00 3297 169 0.1504 0.1699 REMARK 3 4 2.8037 - 2.5475 1.00 3295 180 0.1482 0.1656 REMARK 3 5 2.5475 - 2.3650 1.00 3278 157 0.1445 0.1730 REMARK 3 6 2.3650 - 2.2256 1.00 3256 177 0.1344 0.1578 REMARK 3 7 2.2256 - 2.1142 1.00 3245 178 0.1273 0.1568 REMARK 3 8 2.1142 - 2.0222 1.00 3228 185 0.1246 0.1532 REMARK 3 9 2.0222 - 1.9443 1.00 3240 161 0.1206 0.1580 REMARK 3 10 1.9443 - 1.8772 1.00 3242 152 0.1149 0.1502 REMARK 3 11 1.8772 - 1.8186 1.00 3239 169 0.1126 0.1557 REMARK 3 12 1.8186 - 1.7666 1.00 3191 173 0.1099 0.1546 REMARK 3 13 1.7666 - 1.7201 1.00 3210 179 0.1069 0.1464 REMARK 3 14 1.7201 - 1.6781 0.99 3209 172 0.1019 0.1433 REMARK 3 15 1.6781 - 1.6400 0.99 3158 179 0.0996 0.1378 REMARK 3 16 1.6400 - 1.6051 0.99 3189 175 0.1003 0.1488 REMARK 3 17 1.6051 - 1.5730 0.99 3165 155 0.1018 0.1490 REMARK 3 18 1.5730 - 1.5433 0.99 3174 168 0.1038 0.1369 REMARK 3 19 1.5433 - 1.5157 0.99 3163 158 0.0978 0.1397 REMARK 3 20 1.5157 - 1.4900 0.98 3164 160 0.1049 0.1353 REMARK 3 21 1.4900 - 1.4660 0.98 3112 185 0.1100 0.1660 REMARK 3 22 1.4660 - 1.4434 0.98 3100 171 0.1152 0.1606 REMARK 3 23 1.4434 - 1.4222 0.97 3148 154 0.1170 0.1520 REMARK 3 24 1.4222 - 1.4022 0.97 3087 169 0.1235 0.1684 REMARK 3 25 1.4022 - 1.3832 0.95 3048 161 0.1303 0.1771 REMARK 3 26 1.3832 - 1.3653 0.95 3025 158 0.1376 0.1806 REMARK 3 27 1.3653 - 1.3482 0.91 2884 159 0.1482 0.1842 REMARK 3 28 1.3482 - 1.3320 0.82 2648 153 0.1598 0.2018 REMARK 3 29 1.3320 - 1.3165 0.78 2453 123 0.1618 0.1947 REMARK 3 30 1.3165 - 1.3017 0.70 2249 113 0.1701 0.2118 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.50 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 : 0.008 3877 REMARK 3 ANGLE : 1.275 5302 REMARK 3 CHIRALITY : 0.080 589 REMARK 3 PLANARITY : 0.006 712 REMARK 3 DIHEDRAL : 14.386 1373 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 4RAW 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_1000087117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-12 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) : 0.97926 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 : 98575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 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 (%) : 96.5 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41800 REMARK 200 FOR SHELL : 2.090 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 3Q6X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M TRIS PH REMARK 280 7.0, 30 %(W/V) PEG 3000, 5 MM CADMIUM CHLORIDE, 200MG/ML REMARK 280 AMPICILLIN, VAPOR 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 19.55700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.90750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.38450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.90750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.55700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.38450 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 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 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 SER B 28 REMARK 465 ASN B 29 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 90 143.90 72.49 REMARK 500 HIS A 120 171.73 177.61 REMARK 500 PHE B 70 -42.16 -136.36 REMARK 500 ASP B 90 143.32 73.52 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 CD A 302 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 99.6 REMARK 620 3 HIS A 189 NE2 99.1 123.7 REMARK 620 4 ZZ7 A 301 OXT 172.0 86.0 82.2 REMARK 620 5 HOH A 570 O 89.3 120.2 112.6 83.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 303 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 94.9 REMARK 620 3 HIS A 250 NE2 89.6 111.4 REMARK 620 4 ZZ7 A 301 O1 167.7 96.6 90.4 REMARK 620 5 ZZ7 A 301 N3 93.5 130.2 117.6 75.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 302 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 101.2 REMARK 620 3 HIS B 189 NE2 96.4 124.7 REMARK 620 4 ZZ7 B 301 OXT 172.6 85.3 82.5 REMARK 620 5 HOH B 401 O 90.0 120.3 111.6 83.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 303 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 95.3 REMARK 620 3 HIS B 250 NE2 88.8 111.3 REMARK 620 4 ZZ7 B 301 O1 168.5 95.4 91.3 REMARK 620 5 ZZ7 B 301 N3 93.2 130.4 117.6 76.6 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 CD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD 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 ZZ7 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 303 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: 4RAM RELATED DB: PDB REMARK 900 NDM1, DELTA-30, M67V MUTANT. COMPLEX WITH PENICILLIN G REMARK 900 RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK DBREF 4RAW A 31 270 UNP C7C422 BLAN1_KLEPN 31 270 DBREF 4RAW B 31 270 UNP C7C422 BLAN1_KLEPN 31 270 SEQADV 4RAW SER A 28 UNP C7C422 EXPRESSION TAG SEQADV 4RAW ASN A 29 UNP C7C422 EXPRESSION TAG SEQADV 4RAW ALA A 30 UNP C7C422 EXPRESSION TAG SEQADV 4RAW VAL A 67 UNP C7C422 MET 67 ENGINEERED MUTATION SEQADV 4RAW SER B 28 UNP C7C422 EXPRESSION TAG SEQADV 4RAW ASN B 29 UNP C7C422 EXPRESSION TAG SEQADV 4RAW ALA B 30 UNP C7C422 EXPRESSION TAG SEQADV 4RAW 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 ZZ7 A 301 25 HET CD A 302 1 HET CD A 303 1 HET EDO A 304 4 HET ZZ7 B 301 25 HET CD B 302 1 HET CD B 303 1 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 CD CADMIUM 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 CD 4(CD 2+) FORMUL 6 EDO C2 H6 O2 FORMUL 10 HOH *373(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 PHE A 51 N GLN A 44 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 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 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 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 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 CD CD A 302 1555 1555 2.20 LINK ND1 HIS A 122 CD CD A 302 1555 1555 2.08 LINK OD2 ASP A 124 CD CD A 303 1555 1555 2.17 LINK NE2 HIS A 189 CD CD A 302 1555 1555 2.09 LINK SG CYS A 208 CD CD A 303 1555 1555 2.39 LINK NE2 HIS A 250 CD CD A 303 1555 1555 2.12 LINK OXT ZZ7 A 301 CD CD A 302 1555 1555 2.41 LINK O1 ZZ7 A 301 CD CD A 303 1555 1555 2.20 LINK N3 ZZ7 A 301 CD CD A 303 1555 1555 2.23 LINK CD CD A 302 O HOH A 570 1555 1555 2.05 LINK NE2 HIS B 120 CD CD B 302 1555 1555 2.18 LINK ND1 HIS B 122 CD CD B 302 1555 1555 2.05 LINK OD2 ASP B 124 CD CD B 303 1555 1555 2.17 LINK NE2 HIS B 189 CD CD B 302 1555 1555 2.10 LINK SG CYS B 208 CD CD B 303 1555 1555 2.38 LINK NE2 HIS B 250 CD CD B 303 1555 1555 2.10 LINK OXT ZZ7 B 301 CD CD B 302 1555 1555 2.39 LINK O1 ZZ7 B 301 CD CD B 303 1555 1555 2.21 LINK N3 ZZ7 B 301 CD CD B 303 1555 1555 2.24 LINK CD CD B 302 O HOH B 401 1555 1555 2.07 SITE 1 AC1 20 LEU A 65 TRP A 93 HIS A 122 GLN A 123 SITE 2 AC1 20 ASP A 124 HIS A 189 CYS A 208 LYS A 211 SITE 3 AC1 20 GLY A 219 ASN A 220 HIS A 250 CD A 302 SITE 4 AC1 20 CD A 303 HOH A 439 HOH A 453 HOH A 570 SITE 5 AC1 20 HOH A 585 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 570 SITE 1 AC3 5 ASP A 124 CYS A 208 HIS A 250 ZZ7 A 301 SITE 2 AC3 5 HOH A 570 SITE 1 AC4 8 ASN A 110 ILE A 198 ASP A 199 THR A 201 SITE 2 AC4 8 ILE A 203 ALA A 243 HOH A 435 HOH A 595 SITE 1 AC5 20 THR A 34 PRO A 68 GLY A 69 LEU B 65 SITE 2 AC5 20 TRP B 93 HIS B 122 GLN B 123 ASP B 124 SITE 3 AC5 20 HIS B 189 CYS B 208 LYS B 211 GLY B 219 SITE 4 AC5 20 ASN B 220 HIS B 250 CD B 302 CD B 303 SITE 5 AC5 20 HOH B 401 HOH B 453 HOH B 454 HOH B 488 SITE 1 AC6 5 HIS B 120 HIS B 122 HIS B 189 ZZ7 B 301 SITE 2 AC6 5 HOH B 401 SITE 1 AC7 5 ASP B 124 CYS B 208 HIS B 250 ZZ7 B 301 SITE 2 AC7 5 HOH B 401 CRYST1 39.114 78.769 133.815 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 0.025566 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007473 0.00000