HEADER HYDROLASE/ANTIBIOTIC 07-SEP-12 4H0D TITLE NEW DELHI METALLO-BETA-LACTAMASE-1 COMPLEXED WITH MN FROM KLEBSIELLA TITLE 2 PNEUMONIAE 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 FOLD, KEYWDS 4 HYDROLASE, HYDROLASE-ANTIBIOTICS COMPLEX, HYDROLASE-ANTIBIOTIC KEYWDS 5 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,C.TESAR,R.JEDRZEJCZAK,J.BABNIGG,T.A.BINKOWSKI,J.MIRE, AUTHOR 2 J.SACCHETTINI,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 3 (MCSG),STRUCTURES OF MTB PROTEINS CONFERRING SUSCEPTIBILITY TO KNOWN AUTHOR 4 MTB INHIBITORS (MTBI) REVDAT 2 28-FEB-24 4H0D 1 REMARK SEQADV LINK REVDAT 1 26-SEP-12 4H0D 0 JRNL AUTH Y.KIM,C.TESAR,R.JEDRZEJCZAK,J.BABNIGG,T.A.BINKOWSKI,J.MIRE, JRNL AUTH 2 J.SACCHETTINI,A.JOACHIMIAK JRNL TITL NEW DELHI METALLO-BETA-LACTAMASE-1 COMPLEXED WITH MN FROM JRNL TITL 2 KLEBSIELLA PNEUMONIAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 67022 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3398 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 38.7845 - 4.3186 0.99 2869 152 0.1431 0.1465 REMARK 3 2 4.3186 - 3.4285 1.00 2795 118 0.1233 0.1613 REMARK 3 3 3.4285 - 2.9953 1.00 2723 126 0.1339 0.1626 REMARK 3 4 2.9953 - 2.7215 1.00 2715 133 0.1370 0.1570 REMARK 3 5 2.7215 - 2.5265 1.00 2683 147 0.1251 0.1420 REMARK 3 6 2.5265 - 2.3776 1.00 2674 142 0.1191 0.1588 REMARK 3 7 2.3776 - 2.2585 1.00 2650 151 0.1102 0.1583 REMARK 3 8 2.2585 - 2.1602 1.00 2658 137 0.1054 0.1558 REMARK 3 9 2.1602 - 2.0770 1.00 2654 143 0.1002 0.1504 REMARK 3 10 2.0770 - 2.0054 1.00 2662 143 0.0961 0.1470 REMARK 3 11 2.0054 - 1.9427 1.00 2636 137 0.0958 0.1381 REMARK 3 12 1.9427 - 1.8871 1.00 2625 163 0.0952 0.1521 REMARK 3 13 1.8871 - 1.8375 1.00 2612 168 0.0953 0.1463 REMARK 3 14 1.8375 - 1.7926 1.00 2637 133 0.0982 0.1737 REMARK 3 15 1.7926 - 1.7519 1.00 2639 154 0.1053 0.1692 REMARK 3 16 1.7519 - 1.7146 1.00 2622 143 0.1013 0.1599 REMARK 3 17 1.7146 - 1.6803 1.00 2629 130 0.0987 0.1629 REMARK 3 18 1.6803 - 1.6486 1.00 2630 147 0.1038 0.1792 REMARK 3 19 1.6486 - 1.6191 1.00 2619 137 0.1099 0.1975 REMARK 3 20 1.6191 - 1.5917 1.00 2618 167 0.1141 0.1929 REMARK 3 21 1.5917 - 1.5660 1.00 2597 123 0.1158 0.1847 REMARK 3 22 1.5660 - 1.5419 1.00 2654 140 0.1231 0.2124 REMARK 3 23 1.5419 - 1.5192 1.00 2582 151 0.1330 0.1930 REMARK 3 24 1.5192 - 1.4978 0.92 2441 113 0.1442 0.2414 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3924 REMARK 3 ANGLE : 1.132 5365 REMARK 3 CHIRALITY : 0.079 590 REMARK 3 PLANARITY : 0.005 720 REMARK 3 DIHEDRAL : 14.527 1398 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 4H0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97924 REMARK 200 MONOCHROMATOR : DUOBLE 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 : 67113 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.498 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.66400 REMARK 200 FOR SHELL : 2.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M HEPES PH REMARK 280 7.5, 25 % W/V POLYETHYLENE GLYCOL 3,350, 10 MM MANGANESE REMARK 280 CHLORIDE, 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 19.55050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.85550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.30300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.85550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.55050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.30300 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 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 581 O HOH A 610 2.19 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 90 143.10 72.75 REMARK 500 ASP B 82 -119.00 -119.83 REMARK 500 ASP B 90 142.61 73.34 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 MN A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 94.7 REMARK 620 3 HIS A 189 NE2 96.2 129.6 REMARK 620 4 ZZ7 A 301 OXT 173.6 89.5 84.7 REMARK 620 5 HOH A 402 O 84.0 123.7 106.3 89.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 303 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 98.6 REMARK 620 3 HIS A 250 NE2 90.5 107.5 REMARK 620 4 ZZ7 A 301 O1 165.4 95.9 86.5 REMARK 620 5 ZZ7 A 301 N3 94.5 135.9 114.3 73.8 REMARK 620 6 HOH A 402 O 76.3 71.4 166.3 107.3 71.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 306 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 227 OE1 REMARK 620 2 HIS A 228 NE2 86.2 REMARK 620 3 HIS A 228 NE2 75.5 17.5 REMARK 620 4 HOH A 593 O 74.4 95.4 105.3 REMARK 620 5 GLU B 152 OE2 73.9 73.8 57.8 147.0 REMARK 620 6 ASP B 223 OD2 83.6 169.3 152.9 85.1 100.0 REMARK 620 7 HOH B 427 O 161.2 112.3 123.2 99.7 113.3 78.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 306 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 95 OD2 REMARK 620 2 ASP B 130 OD2 97.5 REMARK 620 3 HOH B 405 O 96.0 83.2 REMARK 620 4 HOH B 623 O 86.2 170.4 87.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 94.5 REMARK 620 3 HIS B 189 NE2 94.2 126.9 REMARK 620 4 ZZ7 B 301 OXT 173.6 90.1 86.6 REMARK 620 5 HOH B 402 O 85.0 125.2 107.7 88.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 303 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 98.6 REMARK 620 3 HIS B 250 NE2 88.3 109.0 REMARK 620 4 ZZ7 B 301 O1 165.5 95.8 88.2 REMARK 620 5 ZZ7 B 301 N3 95.4 134.7 114.3 73.4 REMARK 620 6 HOH B 402 O 75.7 71.7 163.8 108.0 70.5 REMARK 620 N 1 2 3 4 5 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 MN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN 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 GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZZ7 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA 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: 4GYU RELATED DB: PDB REMARK 900 NDM1, DELTA-30 CONSTRUCT, A121F MUTANT REMARK 900 RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK DBREF 4H0D A 31 270 UNP C7C422 BLAN1_KLEPN 31 270 DBREF 4H0D B 31 270 UNP C7C422 BLAN1_KLEPN 31 270 SEQADV 4H0D SER A 28 UNP C7C422 EXPRESSION TAG SEQADV 4H0D ASN A 29 UNP C7C422 EXPRESSION TAG SEQADV 4H0D ALA A 30 UNP C7C422 EXPRESSION TAG SEQADV 4H0D SER B 28 UNP C7C422 EXPRESSION TAG SEQADV 4H0D ASN B 29 UNP C7C422 EXPRESSION TAG SEQADV 4H0D 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 MN A 302 1 HET MN A 303 1 HET EDO A 304 4 HET GOL A 305 6 HET MN A 306 1 HET ZZ7 B 301 25 HET MN B 302 1 HET MN B 303 1 HET FMT B 304 3 HET SO4 B 305 5 HET NA B 306 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 MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM FMT FORMIC ACID HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETSYN ZZ7 AMPICILLIN (OPEN FORM) HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZZ7 2(C16 H21 N3 O5 S) FORMUL 4 MN 5(MN 2+) FORMUL 6 EDO C2 H6 O2 FORMUL 7 GOL C3 H8 O3 FORMUL 12 FMT C H2 O2 FORMUL 13 SO4 O4 S 2- FORMUL 14 NA NA 1+ FORMUL 15 HOH *469(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 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 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 GLN B 44 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 GLY B 71 N MET 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 GLY B 207 -1 O PHE B 205 N VAL B 196 SHEET 4 D 4 MET B 245 MET B 248 1 O VAL B 247 N GLY B 206 LINK NE2 HIS A 120 MN MN A 302 1555 1555 2.26 LINK ND1 HIS A 122 MN MN A 302 1555 1555 2.15 LINK OD2 ASP A 124 MN MN A 303 1555 1555 2.13 LINK NE2 HIS A 189 MN MN A 302 1555 1555 2.19 LINK SG CYS A 208 MN MN A 303 1555 1555 2.50 LINK OE1AGLU A 227 MN MN A 306 1555 1555 2.54 LINK NE2AHIS A 228 MN MN A 306 1555 1555 2.20 LINK NE2BHIS A 228 MN MN A 306 1555 1555 2.63 LINK NE2 HIS A 250 MN MN A 303 1555 1555 2.13 LINK OXT ZZ7 A 301 MN MN A 302 1555 1555 2.14 LINK O1 ZZ7 A 301 MN MN A 303 1555 1555 2.19 LINK N3 ZZ7 A 301 MN MN A 303 1555 1555 2.34 LINK MN MN A 302 O HOH A 402 1555 1555 2.08 LINK MN MN A 303 O HOH A 402 1555 1555 2.79 LINK MN MN A 306 O HOH A 593 1555 1555 2.76 LINK MN MN A 306 OE2 GLU B 152 1555 1555 2.59 LINK MN MN A 306 OD2 ASP B 223 1555 1555 2.35 LINK MN MN A 306 O HOH B 427 1555 1555 2.18 LINK OD2 ASP B 95 NA NA B 306 1555 1555 2.25 LINK NE2 HIS B 120 MN MN B 302 1555 1555 2.24 LINK ND1 HIS B 122 MN MN B 302 1555 1555 2.13 LINK OD2 ASP B 124 MN MN B 303 1555 1555 2.13 LINK OD2 ASP B 130 NA NA B 306 1555 1555 2.41 LINK NE2 HIS B 189 MN MN B 302 1555 1555 2.16 LINK SG CYS B 208 MN MN B 303 1555 1555 2.49 LINK NE2 HIS B 250 MN MN B 303 1555 1555 2.18 LINK OXT ZZ7 B 301 MN MN B 302 1555 1555 2.17 LINK O1 ZZ7 B 301 MN MN B 303 1555 1555 2.19 LINK N3 ZZ7 B 301 MN MN B 303 1555 1555 2.37 LINK MN MN B 302 O HOH B 402 1555 1555 2.09 LINK MN MN B 303 O HOH B 402 1555 1555 2.79 LINK NA NA B 306 O HOH B 405 1555 1555 2.42 LINK NA NA B 306 O HOH B 623 1555 1555 2.40 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 MN A 302 MN A 303 HOH A 402 HOH A 436 SITE 5 AC1 20 HOH A 455 HOH A 518 THR B 34 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 402 SITE 1 AC3 5 ASP A 124 CYS A 208 HIS A 250 ZZ7 A 301 SITE 2 AC3 5 HOH A 402 SITE 1 AC4 3 PRO A 253 SER A 255 GOL A 305 SITE 1 AC5 4 ASP A 95 ASP A 130 EDO A 304 HOH A 644 SITE 1 AC6 7 GLU A 227 HIS A 228 HOH A 593 GLU B 152 SITE 2 AC6 7 ASP B 223 FMT B 304 HOH B 427 SITE 1 AC7 20 THR A 34 PRO A 68 GLY A 69 LEU B 65 SITE 2 AC7 20 MET B 67 TRP B 93 HIS B 122 GLN B 123 SITE 3 AC7 20 ASP B 124 HIS B 189 CYS B 208 LYS B 211 SITE 4 AC7 20 GLY B 219 ASN B 220 HIS B 250 MN B 302 SITE 5 AC7 20 MN B 303 HOH B 402 HOH B 426 HOH B 557 SITE 1 AC8 5 HIS B 120 HIS B 122 HIS B 189 ZZ7 B 301 SITE 2 AC8 5 HOH B 402 SITE 1 AC9 5 ASP B 124 CYS B 208 HIS B 250 ZZ7 B 301 SITE 2 AC9 5 HOH B 402 SITE 1 BC1 6 GLU A 227 MN A 306 HIS B 122 GLU B 152 SITE 2 BC1 6 ASP B 223 HOH B 503 SITE 1 BC2 3 ARG A 264 LYS A 268 ARG B 270 SITE 1 BC3 5 ASP B 95 ASP B 130 HOH B 405 HOH B 467 SITE 2 BC3 5 HOH B 623 CRYST1 39.101 78.606 133.711 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 0.025575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007479 0.00000