HEADER HYDROLASE 20-DEC-06 2JC7 TITLE THE CRYSTAL STRUCTURE OF THE CARBAPENEMASE OXA-24 REVEALS NEW INSIGHTS TITLE 2 INTO THE MECHANISM OF CARBAPENEM-HYDROLYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE OXA-24; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 32-275; COMPND 5 SYNONYM: OXA40, CARBAPENEM-HYDROLYZING BETA-LACTAMASE OXA-40, BETA- COMPND 6 LACTAMASE, OXA-24 CARBAPENEMASE; COMPND 7 EC: 3.5.2.6; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS PLASMID, B-LACTAMASES, ENZYME MECHANISM, CARBAPENEM RESISTANCE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SANTILLANA,A.ROMERO REVDAT 5 13-DEC-23 2JC7 1 REMARK REVDAT 4 24-FEB-09 2JC7 1 VERSN REVDAT 3 10-APR-07 2JC7 1 JRNL REVDAT 2 03-APR-07 2JC7 1 JRNL REVDAT 1 20-MAR-07 2JC7 0 JRNL AUTH E.SANTILLANA,A.BECEIRO,G.BOU,A.ROMERO JRNL TITL CRYSTAL STRUCTURE OF THE CARBAPENEMASE OXA-24 REVEALS JRNL TITL 2 INSIGHTS INTO THE MECHANISM OF CARBAPENEM HYDROLYSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 5354 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17374723 JRNL DOI 10.1073/PNAS.0607557104 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1439570.960 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1266 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2443 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 205 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1932 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.62000 REMARK 3 B22 (A**2) : -8.62000 REMARK 3 B33 (A**2) : 17.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.240 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.330 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.430 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 35.45 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JC7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1290030861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16630 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 55.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 13.40 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1K57 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 2 M AMMONIUM REMARK 280 SULFATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 43.05000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.10000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.52500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.10000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.10000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.57500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.10000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.10000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.52500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.10000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.10000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.57500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.05000 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: PQS 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 109 CG CD CE NZ 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 69 58.98 -151.92 REMARK 500 ALA A 80 -145.54 51.68 REMARK 500 THR A 157 16.61 53.06 REMARK 500 ASN A 165 11.66 -158.50 REMARK 500 LEU A 232 95.82 -166.03 REMARK 500 ASN A 240 3.19 -66.73 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 SO4 A1276 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 1 TO 21 COMPRISED THE SIGNAL PEPTIDE AND ARE NOT REMARK 999 PRESENT IN THE RECOMBINANT PROTEIN EXPRESSED TO OBTAIN REMARK 999 THE 3D STRUCTURE.PROTEIN_ID: CAB92323, EMBL NUCLEOTIDE REMARK 999 ACCESSION NUMBER: AJ239129 DBREF 2JC7 A 32 275 UNP Q8RLA6 Q8RLA6_ACIBA 32 275 SEQRES 1 A 244 HIS ILE SER SER GLN GLN HIS GLU LYS ALA ILE LYS SER SEQRES 2 A 244 TYR PHE ASP GLU ALA GLN THR GLN GLY VAL ILE ILE ILE SEQRES 3 A 244 LYS GLU GLY LYS ASN LEU SER THR TYR GLY ASN ALA LEU SEQRES 4 A 244 ALA ARG ALA ASN LYS GLU TYR VAL PRO ALA SER THR PHE SEQRES 5 A 244 LYS MET LEU ASN ALA LEU ILE GLY LEU GLU ASN HIS LYS SEQRES 6 A 244 ALA THR THR ASN GLU ILE PHE LYS TRP ASP GLY LYS LYS SEQRES 7 A 244 ARG THR TYR PRO MET TRP GLU LYS ASP MET THR LEU GLY SEQRES 8 A 244 GLU ALA MET ALA LEU SER ALA VAL PRO VAL TYR GLN GLU SEQRES 9 A 244 LEU ALA ARG ARG THR GLY LEU GLU LEU MET GLN LYS GLU SEQRES 10 A 244 VAL LYS ARG VAL ASN PHE GLY ASN THR ASN ILE GLY THR SEQRES 11 A 244 GLN VAL ASP ASN PHE TRP LEU VAL GLY PRO LEU LYS ILE SEQRES 12 A 244 THR PRO VAL GLN GLU VAL ASN PHE ALA ASP ASP LEU ALA SEQRES 13 A 244 HIS ASN ARG LEU PRO PHE LYS LEU GLU THR GLN GLU GLU SEQRES 14 A 244 VAL LYS LYS MET LEU LEU ILE LYS GLU VAL ASN GLY SER SEQRES 15 A 244 LYS ILE TYR ALA LYS SER GLY TRP GLY MET GLY VAL THR SEQRES 16 A 244 PRO GLN VAL GLY TRP LEU THR GLY TRP VAL GLU GLN ALA SEQRES 17 A 244 ASN GLY LYS LYS ILE PRO PHE SER LEU ASN LEU GLU MET SEQRES 18 A 244 LYS GLU GLY MET SER GLY SER ILE ARG ASN GLU ILE THR SEQRES 19 A 244 TYR LYS SER LEU GLU ASN LEU GLY ILE ILE HET SO4 A1276 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *121(H2 O) HELIX 1 1 SER A 34 ALA A 49 1 16 HELIX 2 2 ALA A 69 LYS A 75 5 7 HELIX 3 3 PRO A 79 THR A 82 5 4 HELIX 4 4 PHE A 83 ASN A 94 1 12 HELIX 5 5 TYR A 112 GLU A 116 5 5 HELIX 6 6 THR A 120 SER A 128 1 9 HELIX 7 7 ALA A 129 GLY A 141 1 13 HELIX 8 8 GLY A 141 ASN A 153 1 13 HELIX 9 9 ASN A 165 GLY A 170 1 6 HELIX 10 10 THR A 175 HIS A 188 1 14 HELIX 11 11 LYS A 194 MET A 204 1 11 HELIX 12 12 SER A 259 LEU A 272 1 14 SHEET 1 AA 6 ASN A 62 GLY A 67 0 SHEET 2 AA 6 GLY A 53 GLU A 59 -1 O ILE A 55 N TYR A 66 SHEET 3 AA 6 LYS A 243 MET A 252 -1 O PRO A 245 N LYS A 58 SHEET 4 AA 6 GLN A 228 GLU A 237 -1 O GLN A 228 N MET A 252 SHEET 5 AA 6 SER A 213 GLY A 222 -1 O LYS A 214 N GLU A 237 SHEET 6 AA 6 LEU A 206 VAL A 210 -1 N ILE A 207 O ILE A 215 CISPEP 1 GLY A 170 PRO A 171 0 0.38 CISPEP 2 THR A 226 PRO A 227 0 -0.18 SITE 1 AC1 9 SER A 81 SER A 128 SER A 219 GLY A 220 SITE 2 AC1 9 TRP A 221 ARG A 261 HOH A2041 HOH A2120 SITE 3 AC1 9 HOH A2121 CRYST1 102.200 102.200 86.100 90.00 90.00 90.00 P 41 21 2 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 0.009785 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011614 0.00000