HEADER HYDROLASE 16-JAN-14 4OH0 TITLE CRYSTAL STRUCTURE OF OXA-58 CARBAPENEMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE OXA-58; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBAPENEM-HYDROLYZING BETA-LACTAMASE OXA-58, CARBAPENEM- COMPND 5 HYDROLYZING OXACILLINASE, CARBAPENEM-HYDROLYZING OXACILLINASE OXA-58, COMPND 6 OXA-58, OXA-58 OXACILLINASE; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: BLAOXA-58, BLA-OXA-58, BLA-OXA58; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-LACTAMASE, ANTIBIOTIC RESISTANCE, CARBOXYLATED LYSINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SMITH,N.T.ANTUNES,M.TOTH,S.B.VAKULENKO REVDAT 2 02-APR-14 4OH0 1 JRNL REVDAT 1 26-FEB-14 4OH0 0 JRNL AUTH C.A.SMITH,N.T.ANTUNES,M.TOTH,S.B.VAKULENKO JRNL TITL CRYSTAL STRUCTURE OF CARBAPENEMASE OXA-58 FROM ACINETOBACTER JRNL TITL 2 BAUMANNII. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 58 2135 2014 JRNL REFN ISSN 0066-4804 JRNL PMID 24468777 JRNL DOI 10.1128/AAC.01983-13 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : 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) : 38.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 56877 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2890 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 38.1195 - 3.5857 1.00 2776 149 0.1488 0.1616 REMARK 3 2 3.5857 - 2.8464 0.99 2633 139 0.1568 0.1947 REMARK 3 3 2.8464 - 2.4866 1.00 2639 126 0.1664 0.1965 REMARK 3 4 2.4866 - 2.2593 1.00 2590 154 0.1518 0.1804 REMARK 3 5 2.2593 - 2.0974 1.00 2568 148 0.1446 0.1594 REMARK 3 6 2.0974 - 1.9737 1.00 2563 125 0.1429 0.1875 REMARK 3 7 1.9737 - 1.8749 1.00 2576 128 0.1409 0.1540 REMARK 3 8 1.8749 - 1.7933 1.00 2596 115 0.1374 0.1813 REMARK 3 9 1.7933 - 1.7243 1.00 2567 147 0.1343 0.1828 REMARK 3 10 1.7243 - 1.6648 1.00 2557 138 0.1346 0.1827 REMARK 3 11 1.6648 - 1.6127 1.00 2523 151 0.1266 0.1785 REMARK 3 12 1.6127 - 1.5666 1.00 2548 131 0.1254 0.1587 REMARK 3 13 1.5666 - 1.5254 1.00 2569 138 0.1330 0.1589 REMARK 3 14 1.5254 - 1.4881 1.00 2523 132 0.1296 0.1935 REMARK 3 15 1.4881 - 1.4543 1.00 2548 154 0.1433 0.1822 REMARK 3 16 1.4543 - 1.4234 1.00 2534 118 0.1440 0.1646 REMARK 3 17 1.4234 - 1.3949 1.00 2569 128 0.1561 0.2169 REMARK 3 18 1.3949 - 1.3686 1.00 2537 130 0.1621 0.2029 REMARK 3 19 1.3686 - 1.3441 1.00 2523 156 0.1822 0.2215 REMARK 3 20 1.3441 - 1.3213 1.00 2506 136 0.1990 0.2324 REMARK 3 21 1.3213 - 1.3000 1.00 2542 147 0.2108 0.2597 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.10 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 : 0.005 2044 REMARK 3 ANGLE : 1.027 2775 REMARK 3 CHIRALITY : 0.044 298 REMARK 3 PLANARITY : 0.006 361 REMARK 3 DIHEDRAL : 13.963 772 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 4OH0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB084481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56879 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 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) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.79500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 0.1 M TRIS-HCL, REMARK 280 PH 8.5, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K 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 18.56050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.87900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.70400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.87900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.56050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.70400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 LEU A 3 REMARK 465 LEU A 4 REMARK 465 LYS A 5 REMARK 465 ILE A 6 REMARK 465 LEU A 7 REMARK 465 SER A 8 REMARK 465 LEU A 9 REMARK 465 VAL A 10 REMARK 465 CYS A 11 REMARK 465 LEU A 12 REMARK 465 SER A 13 REMARK 465 ILE A 14 REMARK 465 SER A 15 REMARK 465 ILE A 16 REMARK 465 GLY A 17 REMARK 465 ALA A 18 REMARK 465 CYS A 19 REMARK 465 ALA A 20 REMARK 465 GLU A 21 REMARK 465 HIS A 22 REMARK 465 SER A 23 REMARK 465 MET A 24 REMARK 465 SER A 25 REMARK 465 ARG A 26 REMARK 465 ALA A 27 REMARK 465 LYS A 28 REMARK 465 THR A 29 REMARK 465 SER A 30 REMARK 465 THR A 31 REMARK 465 ILE A 32 REMARK 465 PRO A 33 REMARK 465 GLN A 34 REMARK 465 VAL A 35 REMARK 465 ASN A 36 REMARK 465 ASN A 37 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 ALA A 82 -143.76 52.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 301 DBREF 4OH0 A 1 280 UNP Q2TR58 Q2TR58_ACIBA 1 280 SEQRES 1 A 280 MET LYS LEU LEU LYS ILE LEU SER LEU VAL CYS LEU SER SEQRES 2 A 280 ILE SER ILE GLY ALA CYS ALA GLU HIS SER MET SER ARG SEQRES 3 A 280 ALA LYS THR SER THR ILE PRO GLN VAL ASN ASN SER ILE SEQRES 4 A 280 ILE ASP GLN ASN VAL GLN ALA LEU PHE ASN GLU ILE SER SEQRES 5 A 280 ALA ASP ALA VAL PHE VAL THR TYR ASP GLY GLN ASN ILE SEQRES 6 A 280 LYS LYS TYR GLY THR HIS LEU ASP ARG ALA LYS THR ALA SEQRES 7 A 280 TYR ILE PRO ALA SER THR PHE KCX ILE ALA ASN ALA LEU SEQRES 8 A 280 ILE GLY LEU GLU ASN HIS LYS ALA THR SER THR GLU ILE SEQRES 9 A 280 PHE LYS TRP ASP GLY LYS PRO ARG PHE PHE LYS ALA TRP SEQRES 10 A 280 ASP LYS ASP PHE THR LEU GLY GLU ALA MET GLN ALA SER SEQRES 11 A 280 THR VAL PRO VAL TYR GLN GLU LEU ALA ARG ARG ILE GLY SEQRES 12 A 280 PRO SER LEU MET GLN SER GLU LEU GLN ARG ILE GLY TYR SEQRES 13 A 280 GLY ASN MET GLN ILE GLY THR GLU VAL ASP GLN PHE TRP SEQRES 14 A 280 LEU LYS GLY PRO LEU THR ILE THR PRO ILE GLN GLU VAL SEQRES 15 A 280 LYS PHE VAL TYR ASP LEU ALA GLN GLY GLN LEU PRO PHE SEQRES 16 A 280 LYS PRO GLU VAL GLN GLN GLN VAL LYS GLU MET LEU TYR SEQRES 17 A 280 VAL GLU ARG ARG GLY GLU ASN ARG LEU TYR ALA LYS SER SEQRES 18 A 280 GLY TRP GLY MET ALA VAL ASP PRO GLN VAL GLY TRP TYR SEQRES 19 A 280 VAL GLY PHE VAL GLU LYS ALA ASP GLY GLN VAL VAL ALA SEQRES 20 A 280 PHE ALA LEU ASN MET GLN MET LYS ALA GLY ASP ASP ILE SEQRES 21 A 280 ALA LEU ARG LYS GLN LEU SER LEU ASP VAL LEU ASP LYS SEQRES 22 A 280 LEU GLY VAL PHE HIS TYR LEU MODRES 4OH0 KCX A 86 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 86 12 HET CL A 301 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM CL CHLORIDE ION FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 CL CL 1- FORMUL 3 HOH *323(H2 O) HELIX 1 1 SER A 38 GLU A 50 1 13 HELIX 2 2 HIS A 71 THR A 77 5 7 HELIX 3 3 PRO A 81 THR A 84 5 4 HELIX 4 4 PHE A 85 ASN A 96 1 12 HELIX 5 5 PHE A 114 ASP A 118 5 5 HELIX 6 6 THR A 122 SER A 130 1 9 HELIX 7 7 THR A 131 GLY A 143 1 13 HELIX 8 8 GLY A 143 GLY A 155 1 13 HELIX 9 9 GLN A 167 GLY A 172 1 6 HELIX 10 10 THR A 177 GLY A 191 1 15 HELIX 11 11 LYS A 196 LEU A 207 1 12 HELIX 12 12 ALA A 261 LEU A 274 1 14 SHEET 1 A 6 ILE A 65 GLY A 69 0 SHEET 2 A 6 ALA A 55 TYR A 60 -1 N THR A 59 O LYS A 66 SHEET 3 A 6 VAL A 245 MET A 254 -1 O ALA A 247 N TYR A 60 SHEET 4 A 6 GLN A 230 GLU A 239 -1 N GLY A 232 O MET A 252 SHEET 5 A 6 ASN A 215 GLY A 224 -1 N ARG A 216 O GLU A 239 SHEET 6 A 6 TYR A 208 ARG A 212 -1 N GLU A 210 O LEU A 217 LINK C PHE A 85 N KCX A 86 1555 1555 1.33 LINK C KCX A 86 N ILE A 87 1555 1555 1.33 CISPEP 1 GLY A 172 PRO A 173 0 13.45 CISPEP 2 ASP A 228 PRO A 229 0 -7.61 SITE 1 AC1 5 SER A 221 GLY A 222 ARG A 263 HOH A 621 SITE 2 AC1 5 HOH A 706 CRYST1 37.121 65.408 93.758 90.00 90.00 90.00 P 21 21 21 4 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 0.026939 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010666 0.00000