HEADER HYDROLASE 05-SEP-12 4GYQ TITLE CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 D223A MUTANT TITLE 2 FROM KLEBSIELLA PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE NDM-1; COMPND 3 CHAIN: A, B, C, D; 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: 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, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,C.TESAR,R.JEDRZEJCZAK,J.BABNIGG,T.A.BINKOWSKI,J.MIRE, AUTHOR 2 J.SACCHETTINI,A.JOACHIMIAK,MCSG,MIDWEST CENTER FOR STRUCTURAL AUTHOR 3 GENOMICS (MCSG),STRUCTURES OF MTB PROTEINS CONFERRING SUSCEPTIBILITY AUTHOR 4 TO KNOWN MTB INHIBITORS (MTBI) REVDAT 3 13-SEP-23 4GYQ 1 REMARK SEQADV LINK REVDAT 2 24-JAN-18 4GYQ 1 AUTHOR REVDAT 1 26-SEP-12 4GYQ 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 CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 JRNL TITL 2 D223A MUTANT FROM KLEBSIELLA PNEUMONIAE JRNL REF TO BE PUBLISHED 2012 JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_920) 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 162771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 8178 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 34.0464 - 4.1953 0.99 5485 278 0.1583 0.1805 REMARK 3 2 4.1953 - 3.3308 1.00 5371 306 0.1386 0.1519 REMARK 3 3 3.3308 - 2.9100 1.00 5381 315 0.1511 0.1934 REMARK 3 4 2.9100 - 2.6441 1.00 5337 305 0.1467 0.1673 REMARK 3 5 2.6441 - 2.4546 1.00 5376 307 0.1381 0.1760 REMARK 3 6 2.4546 - 2.3099 1.00 5372 256 0.1394 0.1702 REMARK 3 7 2.3099 - 2.1943 1.00 5376 301 0.1329 0.1575 REMARK 3 8 2.1943 - 2.0988 1.00 5361 292 0.1362 0.1771 REMARK 3 9 2.0988 - 2.0180 1.00 5363 260 0.1355 0.1746 REMARK 3 10 2.0180 - 1.9484 1.00 5368 283 0.1303 0.1624 REMARK 3 11 1.9484 - 1.8874 1.00 5391 277 0.1246 0.1736 REMARK 3 12 1.8874 - 1.8335 1.00 5323 296 0.1225 0.1907 REMARK 3 13 1.8335 - 1.7852 1.00 5342 281 0.1243 0.1691 REMARK 3 14 1.7852 - 1.7417 1.00 5348 253 0.1181 0.1666 REMARK 3 15 1.7417 - 1.7021 1.00 5384 283 0.1100 0.1668 REMARK 3 16 1.7021 - 1.6659 1.00 5300 272 0.1080 0.1640 REMARK 3 17 1.6659 - 1.6325 1.00 5385 277 0.1103 0.1669 REMARK 3 18 1.6325 - 1.6017 1.00 5383 257 0.1171 0.2058 REMARK 3 19 1.6017 - 1.5731 1.00 5324 276 0.1341 0.1809 REMARK 3 20 1.5731 - 1.5465 1.00 5356 265 0.1324 0.2022 REMARK 3 21 1.5465 - 1.5215 1.00 5385 278 0.1371 0.1788 REMARK 3 22 1.5215 - 1.4981 1.00 5347 273 0.1399 0.2103 REMARK 3 23 1.4981 - 1.4761 1.00 5327 245 0.1559 0.2196 REMARK 3 24 1.4761 - 1.4553 0.98 5234 298 0.1826 0.2403 REMARK 3 25 1.4553 - 1.4356 0.95 5082 276 0.1958 0.2717 REMARK 3 26 1.4356 - 1.4170 0.91 4882 231 0.2095 0.2432 REMARK 3 27 1.4170 - 1.3993 0.86 4550 287 0.2232 0.2857 REMARK 3 28 1.3993 - 1.3824 0.80 4239 249 0.2492 0.3094 REMARK 3 29 1.3824 - 1.3663 0.73 3865 231 0.2796 0.3079 REMARK 3 30 1.3663 - 1.3510 0.63 3356 170 0.2968 0.3564 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 40.39 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12960 REMARK 3 B22 (A**2) : -1.39720 REMARK 3 B33 (A**2) : 1.52680 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.43250 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 7420 REMARK 3 ANGLE : 1.147 10130 REMARK 3 CHIRALITY : 0.080 1117 REMARK 3 PLANARITY : 0.006 1359 REMARK 3 DIHEDRAL : 12.562 2615 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 4GYQ 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_1000074800. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.97929 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 162811 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 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) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58200 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 35.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS REMARK 280 -TRIS PH 6.5, 25 %(W/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 37.11250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 350 REMARK 350 BIOMOLECULE: 6 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 28 REMARK 465 ASN A 29 REMARK 465 ALA A 30 REMARK 465 ILE A 31 REMARK 465 GLN A 123 REMARK 465 ASP A 124 REMARK 465 LYS A 125 REMARK 465 SER B 28 REMARK 465 ASN B 29 REMARK 465 ALA B 30 REMARK 465 ILE B 31 REMARK 465 ARG B 32 REMARK 465 PRO B 33 REMARK 465 THR B 34 REMARK 465 ILE B 35 REMARK 465 GLY B 36 REMARK 465 GLN B 37 REMARK 465 GLN B 38 REMARK 465 SER C 28 REMARK 465 ASN C 29 REMARK 465 ALA C 30 REMARK 465 ILE C 31 REMARK 465 ARG C 32 REMARK 465 PRO C 33 REMARK 465 SER D 28 REMARK 465 ASN D 29 REMARK 465 ALA D 30 REMARK 465 ILE D 31 REMARK 465 ARG D 32 REMARK 465 PRO D 33 REMARK 465 THR D 34 REMARK 465 ILE D 35 REMARK 465 GLY D 36 REMARK 465 GLN D 37 REMARK 465 GLN D 38 REMARK 465 MET D 39 REMARK 465 GLU D 40 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 PHE A 70 -12.72 -148.33 REMARK 500 ASP A 90 146.19 74.75 REMARK 500 ASP B 90 147.99 74.68 REMARK 500 ASP B 124 -116.43 60.37 REMARK 500 PHE C 70 19.20 -141.84 REMARK 500 ASP C 90 148.28 71.78 REMARK 500 ASP C 124 -120.56 54.45 REMARK 500 PHE D 70 16.86 -142.39 REMARK 500 ASP D 90 150.65 72.25 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 MG C 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY C 178 O REMARK 620 2 HOH C 481 O 91.2 REMARK 620 3 HOH C 501 O 72.9 125.2 REMARK 620 4 HOH C 584 O 95.8 162.5 72.3 REMARK 620 5 HOH C 591 O 168.4 88.5 97.9 87.7 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 EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 301 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: MCSG-APC105101 RELATED DB: TARGETTRACK DBREF 4GYQ A 31 270 UNP C7C422 BLAN1_KLEPN 31 270 DBREF 4GYQ B 31 270 UNP C7C422 BLAN1_KLEPN 31 270 DBREF 4GYQ C 31 270 UNP C7C422 BLAN1_KLEPN 31 270 DBREF 4GYQ D 31 270 UNP C7C422 BLAN1_KLEPN 31 270 SEQADV 4GYQ SER A 28 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ASN A 29 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ALA A 30 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ALA A 223 UNP C7C422 ASP 223 ENGINEERED MUTATION SEQADV 4GYQ SER B 28 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ASN B 29 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ALA B 30 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ALA B 223 UNP C7C422 ASP 223 ENGINEERED MUTATION SEQADV 4GYQ SER C 28 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ASN C 29 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ALA C 30 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ALA C 223 UNP C7C422 ASP 223 ENGINEERED MUTATION SEQADV 4GYQ SER D 28 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ASN D 29 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ALA D 30 UNP C7C422 EXPRESSION TAG SEQADV 4GYQ ALA D 223 UNP C7C422 ASP 223 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 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 ALA 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 ALA 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 SEQRES 1 C 243 SER ASN ALA ILE ARG PRO THR ILE GLY GLN GLN MET GLU SEQRES 2 C 243 THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN SEQRES 3 C 243 LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP SEQRES 4 C 243 MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE SEQRES 5 C 243 VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA SEQRES 6 C 243 TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE SEQRES 7 C 243 LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL SEQRES 8 C 243 THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA SEQRES 9 C 243 LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SEQRES 10 C 243 SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA SEQRES 11 C 243 GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU SEQRES 12 C 243 PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE SEQRES 13 C 243 TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL SEQRES 14 C 243 GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU SEQRES 15 C 243 ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY SEQRES 16 C 243 ALA ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA SEQRES 17 C 243 PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SEQRES 18 C 243 SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS SEQRES 19 C 243 THR ALA ARG MET ALA ASP LYS LEU ARG SEQRES 1 D 243 SER ASN ALA ILE ARG PRO THR ILE GLY GLN GLN MET GLU SEQRES 2 D 243 THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN SEQRES 3 D 243 LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP SEQRES 4 D 243 MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE SEQRES 5 D 243 VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA SEQRES 6 D 243 TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE SEQRES 7 D 243 LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL SEQRES 8 D 243 THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA SEQRES 9 D 243 LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SEQRES 10 D 243 SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA SEQRES 11 D 243 GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU SEQRES 12 D 243 PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE SEQRES 13 D 243 TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL SEQRES 14 D 243 GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU SEQRES 15 D 243 ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY SEQRES 16 D 243 ALA ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA SEQRES 17 D 243 PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SEQRES 18 D 243 SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS SEQRES 19 D 243 THR ALA ARG MET ALA ASP LYS LEU ARG HET EDO A 301 4 HET EDO A 302 4 HET EDO B 301 4 HET MG C 301 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 3(C2 H6 O2) FORMUL 8 MG MG 2+ FORMUL 9 HOH *1049(H2 O) HELIX 1 1 PRO A 33 MET A 39 1 7 HELIX 2 2 THR A 94 ILE A 109 1 16 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 GLY B 128 ALA B 135 1 8 HELIX 11 11 ALA B 143 GLY B 153 1 11 HELIX 12 12 GLU B 170 ALA B 174 5 5 HELIX 13 13 HIS B 228 PHE B 240 1 13 HELIX 14 14 ARG B 256 LYS B 268 1 13 HELIX 15 15 ILE C 35 MET C 39 1 5 HELIX 16 16 THR C 94 ILE C 109 1 16 HELIX 17 17 GLY C 128 ALA C 135 1 8 HELIX 18 18 ALA C 143 GLY C 153 1 11 HELIX 19 19 GLU C 170 ALA C 174 5 5 HELIX 20 20 HIS C 228 PHE C 240 1 13 HELIX 21 21 ARG C 256 LYS C 268 1 13 HELIX 22 22 THR D 94 ILE D 109 1 16 HELIX 23 23 GLY D 127 ALA D 135 1 9 HELIX 24 24 ALA D 143 ALA D 149 1 7 HELIX 25 25 PRO D 150 GLY D 153 5 4 HELIX 26 26 GLU D 170 ALA D 174 5 5 HELIX 27 27 HIS D 228 PHE D 240 1 13 HELIX 28 28 ARG D 256 LYS D 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 LEU A 87 N VAL A 80 SHEET 6 A 8 VAL A 113 VAL A 118 1 O VAL A 117 N VAL A 88 SHEET 7 A 8 ALA A 138 ASN A 142 1 O TYR A 140 N VAL A 118 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 ILE B 79 N TRP B 59 SHEET 5 C 8 ARG B 85 VAL B 89 -1 O ARG B 85 N ASP B 82 SHEET 6 C 8 VAL B 113 VAL B 118 1 O ALA B 114 N VAL B 86 SHEET 7 C 8 ALA B 138 ASN B 142 1 O TYR B 140 N VAL B 118 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 SHEET 1 E 8 GLN C 44 PHE C 46 0 SHEET 2 E 8 LEU C 49 ALA C 55 -1 O PHE C 51 N GLN C 44 SHEET 3 E 8 VAL C 58 MET C 67 -1 O GLN C 60 N ARG C 52 SHEET 4 E 8 GLY C 71 ASP C 82 -1 O GLY C 71 N MET C 67 SHEET 5 E 8 ARG C 85 VAL C 89 -1 O ARG C 85 N ASP C 82 SHEET 6 E 8 VAL C 113 VAL C 118 1 O VAL C 117 N VAL C 88 SHEET 7 E 8 ALA C 138 ASN C 142 1 O TYR C 140 N VAL C 118 SHEET 8 E 8 HIS C 159 LEU C 161 1 O LEU C 161 N ALA C 141 SHEET 1 F 4 LEU C 180 PHE C 183 0 SHEET 2 F 4 THR C 195 ILE C 198 -1 O GLY C 197 N LYS C 181 SHEET 3 F 4 ILE C 203 PHE C 205 -1 O PHE C 205 N VAL C 196 SHEET 4 F 4 MET C 245 VAL C 247 1 O VAL C 247 N ALA C 204 SHEET 1 G 8 GLN D 44 PHE D 46 0 SHEET 2 G 8 LEU D 49 ALA D 55 -1 O PHE D 51 N GLN D 44 SHEET 3 G 8 VAL D 58 MET D 67 -1 O GLN D 60 N ARG D 52 SHEET 4 G 8 GLY D 71 ASP D 82 -1 O ILE D 79 N TRP D 59 SHEET 5 G 8 ARG D 85 VAL D 89 -1 O ARG D 85 N ASP D 82 SHEET 6 G 8 VAL D 113 VAL D 118 1 O VAL D 117 N VAL D 88 SHEET 7 G 8 ALA D 138 ASN D 142 1 O TYR D 140 N VAL D 118 SHEET 8 G 8 HIS D 159 LEU D 161 1 O LEU D 161 N ALA D 141 SHEET 1 H 4 LEU D 180 PHE D 183 0 SHEET 2 H 4 THR D 195 ILE D 198 -1 O GLY D 197 N LYS D 181 SHEET 3 H 4 ILE D 203 PHE D 205 -1 O PHE D 205 N VAL D 196 SHEET 4 H 4 MET D 245 VAL D 247 1 O VAL D 247 N ALA D 204 LINK O GLY C 178 MG MG C 301 1555 1555 2.15 LINK MG MG C 301 O HOH C 481 1555 1555 2.16 LINK MG MG C 301 O HOH C 501 1555 1555 2.32 LINK MG MG C 301 O HOH C 584 1555 1555 2.07 LINK MG MG C 301 O HOH C 591 1555 1555 2.29 SITE 1 AC1 7 GLY A 47 ASP A 48 LEU A 49 ASP A 96 SITE 2 AC1 7 GLN A 97 GLN A 100 ARG B 45 SITE 1 AC2 5 ILE A 198 THR A 201 ASP A 202 ILE A 203 SITE 2 AC2 5 ALA A 243 SITE 1 AC3 3 ASP B 66 MET B 126 HOH B 614 SITE 1 AC4 5 GLY C 178 HOH C 481 HOH C 501 HOH C 584 SITE 2 AC4 5 HOH C 591 CRYST1 69.140 74.225 76.599 90.00 90.11 90.00 P 1 21 1 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 0.014463 0.000000 0.000028 0.00000 SCALE2 0.000000 0.013473 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013055 0.00000