HEADER HYDROLASE 17-MAY-00 1E25 TITLE THE HIGH RESOLUTION STRUCTURE OF PER-1 CLASS A BETA-LACTAMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXTENDED-SPECTRUM BETA-LACTAMASE PER-1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 STRAIN: RNL-1; SOURCE 5 GENE: BLAPER-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PK19 KEYWDS HYDROLASE, ANTIBIOTIC RESISTANCE, CLASS A CEPHALOSPORINASE EXPDTA X-RAY DIFFRACTION AUTHOR S.TRANIER,A.T.BOUTHORS,L.MAVEYRAUD,V.GUILLET,W.SOUGAKOFF,J.P.SAMAMA REVDAT 4 08-MAY-24 1E25 1 REMARK REVDAT 3 24-FEB-09 1E25 1 VERSN REVDAT 2 14-JUN-01 1E25 1 AUTHOR REVDAT 1 06-NOV-00 1E25 0 JRNL AUTH S.TRANIER,A.T.BOUTHORS,L.MAVEYRAUD,V.GUILLET,W.SOUGAKOFF, JRNL AUTH 2 J.P.SAMAMA JRNL TITL THE HIGH RESOLUTION CRYSTAL STRUCTURE FOR CLASS A JRNL TITL 2 BETA-LACTAMASE PER-1 REVEALS THE BASES FOR ITS INCREASE IN JRNL TITL 3 BREADTH OF ACTIVITY JRNL REF J.BIOL.CHEM. V. 275 28075 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10825176 JRNL DOI 10.1074/JBC.M003802200 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1509650.340 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 25707 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) : 0.140 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2533 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3835 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 423 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2142 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.04000 REMARK 3 B22 (A**2) : 1.04000 REMARK 3 B33 (A**2) : -2.08000 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) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 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) : 2.540 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.440 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.400 ; 7.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.820 ; 10.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 66.02 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE 3 C-TERMINAL RESIDUES AND THE FIRST REMARK 3 N-TERMINAL RESIDUE WERE NOT SEEN IN THE DENSITY MAPS REMARK 4 REMARK 4 1E25 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1290004966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-98 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 4.70 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 1.0 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25029 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 24.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.12200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: CNS 0.5, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% (V/V) SATURATED AMMONIUM SULFATE, REMARK 280 1MM DITHIOTHREITOL, 100 MM SODIUM ACETATE, PH4.7, PH 4.70 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 23.44500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.16750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.72250 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 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 400 REMARK 400 COMPOUND REMARK 400 CHAIN A ENGINEERED MUTATION GLY239GLN 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 25 REMARK 465 SER A 298 REMARK 465 PRO A 299 REMARK 465 ASN A 300 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 LEU A 297 CG CD1 CD2 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 GLN A 69 -139.83 52.21 REMARK 500 ASN A 103B 74.13 42.37 REMARK 500 ALA A 106 76.91 -151.44 REMARK 500 GLU A 159 47.45 -94.51 REMARK 500 ARG A 220 -111.96 -97.59 REMARK 500 ALA A 296 -77.25 -72.28 REMARK 500 ALA A 296 -77.25 -71.35 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 A 500 DBREF 1E25 A 25 300 UNP P37321 BLE1_PSEAE 27 308 SEQADV 1E25 GLN A 239 UNP P37321 GLY 244 CLONING ARTIFACT SEQRES 1 A 282 GLN SER PRO LEU LEU LYS GLU GLN ILE GLU SER ILE VAL SEQRES 2 A 282 ILE GLY LYS LYS ALA THR VAL GLY VAL ALA VAL TRP GLY SEQRES 3 A 282 PRO ASP ASP LEU GLU PRO LEU LEU ILE ASN PRO PHE GLU SEQRES 4 A 282 LYS PHE PRO MET GLN SER VAL PHE LYS LEU HIS LEU ALA SEQRES 5 A 282 MET LEU VAL LEU HIS GLN VAL ASP GLN GLY LYS LEU ASP SEQRES 6 A 282 LEU ASN GLN THR VAL ILE VAL ASN ARG ALA LYS VAL LEU SEQRES 7 A 282 GLN ASN THR TRP ALA PRO ILE MET LYS ALA TYR GLN GLY SEQRES 8 A 282 ASP GLU PHE SER VAL PRO VAL GLN GLN LEU LEU GLN TYR SEQRES 9 A 282 SER VAL SER HIS SER ASP ASN VAL ALA CYS ASP LEU LEU SEQRES 10 A 282 PHE GLU LEU VAL GLY GLY PRO ALA ALA LEU HIS ASP TYR SEQRES 11 A 282 ILE GLN SER MET GLY ILE LYS GLU THR ALA VAL VAL ALA SEQRES 12 A 282 ASN GLU ALA GLN MET HIS ALA ASP ASP GLN VAL GLN TYR SEQRES 13 A 282 GLN ASN TRP THR SER MET LYS GLY ALA ALA GLU ILE LEU SEQRES 14 A 282 LYS LYS PHE GLU GLN LYS THR GLN LEU SER GLU THR SER SEQRES 15 A 282 GLN ALA LEU LEU TRP LYS TRP MET VAL GLU THR THR THR SEQRES 16 A 282 GLY PRO GLU ARG LEU LYS GLY LEU LEU PRO ALA GLY THR SEQRES 17 A 282 VAL VAL ALA HIS LYS THR GLY THR SER GLN ILE LYS ALA SEQRES 18 A 282 GLY LYS THR ALA ALA THR ASN ASP LEU GLY ILE ILE LEU SEQRES 19 A 282 LEU PRO ASP GLY ARG PRO LEU LEU VAL ALA VAL PHE VAL SEQRES 20 A 282 LYS ASP SER ALA GLU SER SER ARG THR ASN GLU ALA ILE SEQRES 21 A 282 ILE ALA GLN VAL ALA GLN THR ALA TYR GLN PHE GLU LEU SEQRES 22 A 282 LYS LYS LEU SER ALA LEU SER PRO ASN HET SO4 A 500 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *153(H2 O) HELIX 1 1 SER A 26 ILE A 38 1 13 HELIX 2 2 VAL A 71 GLN A 86 1 16 HELIX 3 3 PRO A 107 TYR A 112 1 6 HELIX 4 4 VAL A 119 SER A 130 1 12 HELIX 5 5 ASP A 131 GLY A 143 1 13 HELIX 6 6 GLY A 143 MET A 155 1 13 HELIX 7 7 ASN A 165 ASP A 172 1 8 HELIX 8 8 GLN A 174 GLN A 178 5 5 HELIX 9 9 SER A 182 GLN A 195 1 14 HELIX 10 10 SER A 200 GLU A 213 1 14 HELIX 11 11 SER A 271 LEU A 297 1 27 SHEET 1 A 5 LEU A 57 ILE A 60 0 SHEET 2 A 5 THR A 43 TRP A 49 -1 N VAL A 48 O LEU A 57 SHEET 3 A 5 PRO A 258 LYS A 266 -1 N LYS A 266 O THR A 43 SHEET 4 A 5 ALA A 243 LEU A 251 -1 N ILE A 250 O LEU A 259 SHEET 5 A 5 VAL A 231 THR A 237 -1 N GLY A 236 O ASN A 245 SHEET 1 B 2 THR A 94 ASN A 98 0 SHEET 2 B 2 GLU A 114 PRO A 118 -1 N VAL A 117 O VAL A 95 SITE 1 AC1 8 SER A 70 SER A 130 LYS A 234 THR A 235 SITE 2 AC1 8 GLY A 236 THR A 237 HOH A2152 HOH A2153 CRYST1 84.600 84.600 46.890 90.00 90.00 90.00 P 43 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 0.011820 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021326 0.00000