HEADER HYDROLASE 27-FEB-13 4JF5 TITLE STRUCTURE OF OXA-23 AT PH 4.1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-LACTAMASE OXA-23, BLAOXA-23, CARBAPENEM-HYDROLYZING COMPND 5 BETA-LACTAMASE OXA-23, CARBAPENEMASE OXA-23, CLASS D BETA-LACTAMASE COMPND 6 OXA-23, CLASS D BETA-LACTAMASE OXA-23, OXA-23, OXA-23 BETA-LACTAMASE, COMPND 7 OXA-23 CARBAPENEMASE; COMPND 8 EC: 3.5.2.6; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: ARI-1, BLA(OXA-23), BLA-OXA-23, BLA-OXA-23, BLAOXA-23, OXA-23, SOURCE 5 OXA-23, OXA23; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-LACTAMASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SMITH,S.B.VAKULENKO REVDAT 3 28-FEB-24 4JF5 1 REMARK REVDAT 2 09-OCT-13 4JF5 1 JRNL REVDAT 1 25-SEP-13 4JF5 0 JRNL AUTH C.A.SMITH,N.T.ANTUNES,N.K.STEWART,M.TOTH,M.KUMARASIRI, JRNL AUTH 2 M.CHANG,S.MOBASHERY,S.B.VAKULENKO JRNL TITL STRUCTURAL BASIS FOR CARBAPENEMASE ACTIVITY OF THE OXA-23 JRNL TITL 2 BETA-LACTAMASE FROM ACINETOBACTER BAUMANNII. JRNL REF CHEM.BIOL. V. 20 1107 2013 JRNL REFN ISSN 1074-5521 JRNL PMID 24012371 JRNL DOI 10.1016/J.CHEMBIOL.2013.07.015 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.190 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 95345 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 9182 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 38.7372 - 3.5724 0.92 5763 340 0.1543 0.1849 REMARK 3 2 3.5724 - 2.8358 0.95 5981 330 0.1536 0.1595 REMARK 3 3 2.8358 - 2.4774 0.97 6169 273 0.1488 0.1780 REMARK 3 4 2.4774 - 2.2509 0.88 5561 282 0.1370 0.1642 REMARK 3 5 2.2509 - 2.0896 0.92 5706 356 0.1233 0.1353 REMARK 3 6 2.0896 - 1.9664 0.95 6023 283 0.1194 0.1387 REMARK 3 7 1.9664 - 1.8679 0.95 6002 333 0.1155 0.1417 REMARK 3 8 1.8679 - 1.7866 0.96 6012 325 0.1127 0.1326 REMARK 3 9 1.7866 - 1.7178 0.96 6031 325 0.1096 0.1392 REMARK 3 10 1.7178 - 1.6586 0.93 5865 288 0.1036 0.1225 REMARK 3 11 1.6586 - 1.6067 0.85 5423 275 0.1017 0.1362 REMARK 3 12 1.6067 - 1.5608 0.92 5816 305 0.1014 0.1430 REMARK 3 13 1.5608 - 1.5197 0.93 5794 325 0.1040 0.1479 REMARK 3 14 1.5197 - 1.4826 0.93 5853 332 0.1078 0.1276 REMARK 3 15 1.4826 - 1.4489 0.93 5911 287 0.1175 0.1312 REMARK 3 16 1.4489 - 1.4181 0.93 5826 327 0.1183 0.1400 REMARK 3 17 1.4181 - 1.3897 0.93 5842 294 0.1285 0.1565 REMARK 3 18 1.3897 - 1.3635 0.93 5906 306 0.1312 0.1443 REMARK 3 19 1.3635 - 1.3391 0.92 5762 291 0.1425 0.1571 REMARK 3 20 1.3391 - 1.3164 0.83 5279 261 0.1704 0.2011 REMARK 3 21 1.3164 - 1.2952 0.89 5580 313 0.1745 0.1889 REMARK 3 22 1.2952 - 1.2753 0.91 5715 335 0.1783 0.1983 REMARK 3 23 1.2753 - 1.2565 0.91 5750 273 0.1889 0.2210 REMARK 3 24 1.2565 - 1.2388 0.92 5851 278 0.1882 0.2175 REMARK 3 25 1.2388 - 1.2221 0.91 5702 307 0.1952 0.2200 REMARK 3 26 1.2221 - 1.2062 0.92 5728 323 0.2002 0.2178 REMARK 3 27 1.2062 - 1.1911 0.91 5727 346 0.2082 0.2091 REMARK 3 28 1.1911 - 1.1768 0.92 5843 263 0.2106 0.2270 REMARK 3 29 1.1768 - 1.1631 0.91 5567 297 0.2292 0.2269 REMARK 3 30 1.1631 - 1.1500 0.85 5445 309 0.2700 0.2749 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) : 14.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.30 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 2093 REMARK 3 ANGLE : 1.342 2839 REMARK 3 CHIRALITY : 0.162 315 REMARK 3 PLANARITY : 0.007 364 REMARK 3 DIHEDRAL : 14.037 821 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 4JF5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.1 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) : 0.88557 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 : 95345 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 38.715 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.990 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 (%): 52.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.06 M CITRIC ACID/0.04 M BIS-TRIS REMARK 280 PROPANE, 16 % PEG3350, PH 4.1, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 66.45950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.82550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 66.45950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.82550 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 GLN A 31 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 58 73.13 41.36 REMARK 500 LYS A 59 -9.85 64.72 REMARK 500 ALA A 78 -146.69 51.49 REMARK 500 ASN A 163 9.24 -150.54 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 FLC 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JF4 RELATED DB: PDB REMARK 900 OXA-23 MEROPENEM COMPLEX REMARK 900 RELATED ID: 4JF6 RELATED DB: PDB DBREF 4JF5 A 31 273 UNP Q9L4P2 Q9L4P2_ACIBA 31 273 SEQRES 1 A 243 GLN ILE VAL GLN GLY HIS ASN GLN VAL ILE HIS GLN TYR SEQRES 2 A 243 PHE ASP GLU LYS ASN THR SER GLY VAL LEU VAL ILE GLN SEQRES 3 A 243 THR ASP LYS LYS ILE ASN LEU TYR GLY ASN ALA LEU SER SEQRES 4 A 243 ARG ALA ASN THR GLU TYR VAL PRO ALA SER THR PHE LYS SEQRES 5 A 243 MET LEU ASN ALA LEU ILE GLY LEU GLU ASN GLN LYS THR SEQRES 6 A 243 ASP ILE ASN GLU ILE PHE LYS TRP LYS GLY GLU LYS ARG SEQRES 7 A 243 SER PHE THR ALA TRP GLU LYS ASP MET THR LEU GLY GLU SEQRES 8 A 243 ALA MET LYS LEU SER ALA VAL PRO VAL TYR GLN GLU LEU SEQRES 9 A 243 ALA ARG ARG ILE GLY LEU ASP LEU MET GLN LYS GLU VAL SEQRES 10 A 243 LYS ARG ILE GLY PHE GLY ASN ALA GLU ILE GLY GLN GLN SEQRES 11 A 243 VAL ASP ASN PHE TRP LEU VAL GLY PRO LEU LYS VAL THR SEQRES 12 A 243 PRO ILE GLN GLU VAL GLU PHE VAL SER GLN LEU ALA HIS SEQRES 13 A 243 THR GLN LEU PRO PHE SER GLU LYS VAL GLN ALA ASN VAL SEQRES 14 A 243 LYS ASN MET LEU LEU LEU GLU GLU SER ASN GLY TYR LYS SEQRES 15 A 243 ILE PHE GLY LYS THR GLY TRP ALA MET ASP ILE LYS PRO SEQRES 16 A 243 GLN VAL GLY TRP LEU THR GLY TRP VAL GLU GLN PRO ASP SEQRES 17 A 243 GLY LYS ILE VAL ALA PHE ALA LEU ASN MET GLU MET ARG SEQRES 18 A 243 SER GLU MET PRO ALA SER ILE ARG ASN GLU LEU LEU MET SEQRES 19 A 243 LYS SER LEU LYS GLN LEU ASN ILE ILE HET FLC A 301 13 HET EDO A 302 4 HETNAM FLC CITRATE ANION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 FLC C6 H5 O7 3- FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *270(H2 O) HELIX 1 1 ILE A 32 LYS A 47 1 16 HELIX 2 2 ALA A 67 THR A 73 5 7 HELIX 3 3 PRO A 77 THR A 80 5 4 HELIX 4 4 PHE A 81 ASN A 92 1 12 HELIX 5 5 PHE A 110 GLU A 114 5 5 HELIX 6 6 THR A 118 LEU A 125 1 8 HELIX 7 7 PRO A 129 GLY A 139 1 11 HELIX 8 8 GLY A 139 GLY A 151 1 13 HELIX 9 9 ASN A 163 GLY A 168 1 6 HELIX 10 10 THR A 173 HIS A 186 1 14 HELIX 11 11 SER A 192 LEU A 203 1 12 HELIX 12 12 SER A 257 LEU A 270 1 14 SHEET 1 A 6 ILE A 61 GLY A 65 0 SHEET 2 A 6 GLY A 51 GLN A 56 -1 N LEU A 53 O TYR A 64 SHEET 3 A 6 ILE A 241 MET A 250 -1 O ALA A 245 N VAL A 54 SHEET 4 A 6 GLN A 226 GLU A 235 -1 N VAL A 234 O VAL A 242 SHEET 5 A 6 TYR A 211 ALA A 220 -1 N PHE A 214 O TRP A 233 SHEET 6 A 6 LEU A 204 SER A 208 -1 N LEU A 205 O ILE A 213 CISPEP 1 GLY A 168 PRO A 169 0 12.22 CISPEP 2 LYS A 224 PRO A 225 0 -6.04 SITE 1 AC1 12 ALA A 78 SER A 79 SER A 126 ALA A 127 SITE 2 AC1 12 LEU A 166 THR A 217 GLY A 218 TRP A 219 SITE 3 AC1 12 ARG A 259 HOH A 426 HOH A 467 HOH A 600 SITE 1 AC2 5 GLN A 42 TRP A 113 GLU A 206 ASN A 260 SITE 2 AC2 5 HOH A 596 CRYST1 132.919 49.651 44.121 90.00 96.97 90.00 C 1 2 1 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 0.007523 0.000000 0.000920 0.00000 SCALE2 0.000000 0.020141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022834 0.00000