HEADER HYDROLASE 03-SEP-98 1BUE TITLE NMC-A CARBAPENEMASE FROM ENTEROBACTER CLOACAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (IMIPENEM-HYDROLYSING BETA-LACTAMASE); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBAPENEMASE, NMC-A; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTER CLOACAE; SOURCE 3 ORGANISM_TAXID: 550; SOURCE 4 STRAIN: NOR-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, ANTIBIOTIC RESISTANCE, CLASS A CARBAPENEMASE EXPDTA X-RAY DIFFRACTION AUTHOR P.SWAREN,L.MAVEYRAUD,S.CABANTOUS,J.D.PEDELACQ,L.MOUREY,J.M.FRERE, AUTHOR 2 J.P.SAMAMA REVDAT 3 30-OCT-24 1BUE 1 REMARK REVDAT 2 24-FEB-09 1BUE 1 VERSN REVDAT 1 02-SEP-99 1BUE 0 JRNL AUTH P.SWAREN,L.MAVEYRAUD,X.RAQUET,S.CABANTOUS,C.DUEZ, JRNL AUTH 2 J.D.PEDELACQ,S.MARIOTTE-BOYER,L.MOUREY,R.LABIA, JRNL AUTH 3 M.H.NICOLAS-CHANOINE,P.NORDMANN,J.M.FRERE,J.P.SAMAMA JRNL TITL X-RAY ANALYSIS OF THE NMC-A BETA-LACTAMASE AT 1.64-A JRNL TITL 2 RESOLUTION, A CLASS A CARBAPENEMASE WITH BROAD SUBSTRATE JRNL TITL 3 SPECIFICITY. JRNL REF J.BIOL.CHEM. V. 273 26714 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9756914 JRNL DOI 10.1074/JBC.273.41.26714 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.MARIOTTE-BOYER,M.H.NICOLAS-CHANOINE,R.LABIA REMARK 1 TITL A KINETIC STUDY OF NMC-A BETA-LACTAMASE, AN AMBLER CLASS A REMARK 1 TITL 2 CARBAPENEMASE ALSO HYDROLYZING CEPHAMYCINS REMARK 1 REF FEMS MICROBIOL.LETT. V. 143 29 1996 REMARK 1 REFN ISSN 0378-1097 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.NAAS,P.NORDMANN REMARK 1 TITL ANALYSIS OF A CARBAPENEM-HYDROLYZING CLASS A BETA-LACTAMASE REMARK 1 TITL 2 FROM ENTEROBACTER CLOACAE AND OF ITS LYSR-TYPE REGULATORY REMARK 1 TITL 3 PROTEIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 91 7693 1994 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 32739 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 : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1623 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2024 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.30 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.16 REMARK 3 LOW RESOLUTION CUTOFF (A) : 31.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.297 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.37 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.126 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NOT APPLICABLE 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 : NULL REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 BULK SOLVENT CORRECTION USED WITH A DENSITY OF 0.34 E-/A**3, REMARK 3 SOLVENT RADIUS OF 0.25 ANGSTROMS AND B FACTORS OF 50 A**2 REMARK 3 REMARK 3 RESIDUES 30 AND 63 HAVE ALTERNATE CONFORMATIONS. RESIDUE REMARK 3 140A WAS INSERTED. REMARK 4 REMARK 4 1BUE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-96 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 5.25 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, CCP4 REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 31.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.19200 REMARK 200 FOR SHELL : 7.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: CCP4, X-PLOR REMARK 200 STARTING MODEL: NOT APPLICABLE REMARK 200 REMARK 200 REMARK: ONE CRYSTAL WAS USED FOR NATIVE LOW RESOLUTION DATA TO 2.9 REMARK 200 ANGSTROMS RESOLUTION, AND A SECOND CRYSTAL WAS USED FOR DATA TO REMARK 200 1.64 ANGSTROMS RESOLUTION. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: INITIAL PROTEIN CONCENTRATION WAS 2.0 REMARK 280 G/L EQUILIBRATED AGAINST 0.200 M MES PH 5.25, 20% (W/V)PEG 1500, REMARK 280 6% (V/V) N-PROPANOL AT 295K. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 39.34500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.34500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.45000 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 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 28 CG CD CE NZ REMARK 470 LYS A 111 CD CE NZ REMARK 470 ASN A 115 CG OD1 ND2 REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 LYS A 253 CD CE NZ REMARK 470 LYS A 273 CG CD CE NZ REMARK 470 LYS A 291 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 CYS A 69 -142.16 56.75 REMARK 500 TYR A 97 30.95 -149.19 REMARK 500 HIS A 105 73.47 62.83 REMARK 500 ARG A 220 -117.48 -107.12 REMARK 500 ASP A 246 139.98 -171.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BUE A 26 291 UNP P52663 BLAN_ENTCL 28 292 SEQRES 1 A 265 ASN THR LYS GLY ILE ASP GLU ILE LYS ASN LEU GLU THR SEQRES 2 A 265 ASP PHE ASN GLY ARG ILE GLY VAL TYR ALA LEU ASP THR SEQRES 3 A 265 GLY SER GLY LYS SER PHE SER TYR ARG ALA ASN GLU ARG SEQRES 4 A 265 PHE PRO LEU CYS SER SER PHE LYS GLY PHE LEU ALA ALA SEQRES 5 A 265 ALA VAL LEU LYS GLY SER GLN ASP ASN ARG LEU ASN LEU SEQRES 6 A 265 ASN GLN ILE VAL ASN TYR ASN THR ARG SER LEU GLU PHE SEQRES 7 A 265 HIS SER PRO ILE THR THR LYS TYR LYS ASP ASN GLY MET SEQRES 8 A 265 SER LEU GLY ASP MET ALA ALA ALA ALA LEU GLN TYR SER SEQRES 9 A 265 ASP ASN GLY ALA THR ASN ILE ILE LEU GLU ARG TYR ILE SEQRES 10 A 265 GLY GLY PRO GLU GLY MET THR LYS PHE MET ARG SER ILE SEQRES 11 A 265 GLY ASP GLU ASP PHE ARG LEU ASP ARG TRP GLU LEU ASP SEQRES 12 A 265 LEU ASN THR ALA ILE PRO GLY ASP GLU ARG ASP THR SER SEQRES 13 A 265 THR PRO ALA ALA VAL ALA LYS SER LEU LYS THR LEU ALA SEQRES 14 A 265 LEU GLY ASN ILE LEU SER GLU HIS GLU LYS GLU THR TYR SEQRES 15 A 265 GLN THR TRP LEU LYS GLY ASN THR THR GLY ALA ALA ARG SEQRES 16 A 265 ILE ARG ALA SER VAL PRO SER ASP TRP VAL VAL GLY ASP SEQRES 17 A 265 LYS THR GLY SER CYS GLY ALA TYR GLY THR ALA ASN ASP SEQRES 18 A 265 TYR ALA VAL VAL TRP PRO LYS ASN ARG ALA PRO LEU ILE SEQRES 19 A 265 ILE SER VAL TYR THR THR LYS ASN GLU LYS GLU ALA LYS SEQRES 20 A 265 HIS GLU ASP LYS VAL ILE ALA GLU ALA SER ARG ILE ALA SEQRES 21 A 265 ILE ASP ASN LEU LYS FORMUL 2 HOH *115(H2 O) HELIX 1 1 ILE A 30 PHE A 40 1 11 HELIX 2 2 CYS A 69 GLN A 85 5 17 HELIX 3 3 PRO A 107 LYS A 111 1 5 HELIX 4 4 LEU A 119 GLN A 128 1 10 HELIX 5 5 ASN A 132 ARG A 140A 1 10 HELIX 6 6 GLY A 144 ILE A 155 1 12 HELIX 7 7 ASP A 168 ASN A 170 5 3 HELIX 8 8 PRO A 183 LEU A 195 1 13 HELIX 9 9 GLU A 201 LYS A 212 1 12 HELIX 10 10 ILE A 221 SER A 224 5 4 HELIX 11 11 ASP A 276 ASN A 289 1 14 SHEET 1 A 5 SER A 56 TYR A 60 0 SHEET 2 A 5 ARG A 43 ASP A 50 -1 N ALA A 48 O PHE A 57 SHEET 3 A 5 LEU A 259 THR A 266 -1 N THR A 266 O ARG A 43 SHEET 4 A 5 ALA A 244 TRP A 251 -1 N VAL A 250 O LEU A 259 SHEET 5 A 5 VAL A 230 SER A 237 -1 N GLY A 236 O ASN A 245 SHEET 1 B 2 ARG A 65 PRO A 67 0 SHEET 2 B 2 THR A 180 THR A 182 -1 N SER A 181 O PHE A 66 SSBOND 1 CYS A 69 CYS A 238 1555 1555 2.03 CISPEP 1 GLU A 166 LEU A 167 0 0.53 CRYST1 78.690 52.900 67.470 90.00 90.00 90.00 P 21 21 2 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 0.012708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014821 0.00000