HEADER HYDROLASE 13-AUG-96 1DJB TITLE STRUCTURE OF BETA-LACTAMASE PRECURSOR, S70A MUTANT, AT 298K COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PENICILLINASE; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: PC1; SOURCE 5 GENE: BLAZ; SOURCE 6 EXPRESSION_SYSTEM: SHUTTLE PLASMID FROM ESCHERICHIA COLI MC1061 TO SOURCE 7 STAPHYLOCOCCUS AUREUS RN4220; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIAL; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTS6; SOURCE 10 EXPRESSION_SYSTEM_GENE: BLAZ KEYWDS HYDROLASE, ANTIBIOTIC RESISTANCE, PLASMID, TRANSPOSABLE ELEMENT EXPDTA X-RAY DIFFRACTION AUTHOR C.C.H.CHEN,O.HERZBERG REVDAT 5 07-FEB-24 1DJB 1 REMARK REVDAT 4 03-NOV-21 1DJB 1 SEQADV REVDAT 3 16-NOV-11 1DJB 1 VERSN HETATM REVDAT 2 24-FEB-09 1DJB 1 VERSN REVDAT 1 12-MAR-97 1DJB 0 JRNL AUTH C.C.CHEN,T.J.SMITH,G.KAPADIA,S.WASCH,L.E.ZAWADZKE,A.COULSON, JRNL AUTH 2 O.HERZBERG JRNL TITL STRUCTURE AND KINETICS OF THE BETA-LACTAMASE MUTANTS S70A JRNL TITL 2 AND K73H FROM STAPHYLOCOCCUS AUREUS PC1. JRNL REF BIOCHEMISTRY V. 35 12251 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8823158 JRNL DOI 10.1021/BI961153V REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.E.ZAWADZKE,T.J.SMITH,O.HERZBERG REMARK 1 TITL AN ENGINEERED STAPHYLOCOCCUS AUREUS PC1 BETA-LACTAMASE THAT REMARK 1 TITL 2 HYDROLYSES THIRD-GENERATION CEPHALOSPORINS REMARK 1 REF PROTEIN ENG. V. 8 1275 1995 REMARK 1 REFN ISSN 0269-2139 REMARK 1 REFERENCE 2 REMARK 1 AUTH O.HERZBERG REMARK 1 TITL REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM REMARK 1 TITL 2 STAPHYLOCOCCUS AUREUS PC1 AT 2.0 REMARK 1 REF J.MOL.BIOL. V. 217 701 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH O.HERZBERG,J.MOULT REMARK 1 TITL BACTERIAL RESISTANCE TO BETA-LACTAM ANTIBIOTICS. CRYSTAL REMARK 1 TITL 2 STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 REMARK 1 TITL 3 AT 2.5 A RESOLUTION REMARK 1 REF SCIENCE V. 236 694 1987 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.7 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14361 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL 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 : 2028 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL 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) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 : 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-91 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18843 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.85000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.65000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 69.15000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.85000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.65000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.15000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.85000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.65000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.15000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.85000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.65000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.15000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 376 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 395 LIES ON A SPECIAL POSITION. 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 PHE A 60 112.87 -162.76 REMARK 500 ALA A 69 -140.66 46.37 REMARK 500 TYR A 105 72.72 59.09 REMARK 500 ASN A 161 78.86 -111.81 REMARK 500 ILE A 194 -64.43 -104.25 REMARK 500 ASN A 196 69.43 -154.50 REMARK 500 LEU A 220 -130.64 -116.26 REMARK 500 ALA A 242 27.69 45.43 REMARK 500 SER A 243 106.37 -59.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 1DJB A 31 290 UNP P00807 BLAC_STAAU 25 281 SEQADV 1DJB ALA A 70 UNP P00807 SER 63 ENGINEERED MUTATION SEQRES 1 A 257 LYS GLU LEU ASN ASP LEU GLU LYS LYS TYR ASN ALA HIS SEQRES 2 A 257 ILE GLY VAL TYR ALA LEU ASP THR LYS SER GLY LYS GLU SEQRES 3 A 257 VAL LYS PHE ASN SER ASP LYS ARG PHE ALA TYR ALA ALA SEQRES 4 A 257 THR SER LYS ALA ILE ASN SER ALA ILE LEU LEU GLU GLN SEQRES 5 A 257 VAL PRO TYR ASN LYS LEU ASN LYS LYS VAL HIS ILE ASN SEQRES 6 A 257 LYS ASP ASP ILE VAL ALA TYR SER PRO ILE LEU GLU LYS SEQRES 7 A 257 TYR VAL GLY LYS ASP ILE THR LEU LYS ALA LEU ILE GLU SEQRES 8 A 257 ALA SER MET THR TYR SER ASP ASN THR ALA ASN ASN LYS SEQRES 9 A 257 ILE ILE LYS GLU ILE GLY GLY ILE LYS LYS VAL LYS GLN SEQRES 10 A 257 ARG LEU LYS GLU LEU GLY ASP LYS VAL THR ASN PRO VAL SEQRES 11 A 257 ARG TYR GLU ILE GLU LEU ASN TYR TYR SER PRO LYS SER SEQRES 12 A 257 LYS LYS ASP THR SER THR PRO ALA ALA PHE GLY LYS THR SEQRES 13 A 257 LEU ASN LYS LEU ILE ALA ASN GLY LYS LEU SER LYS GLU SEQRES 14 A 257 ASN LYS LYS PHE LEU LEU ASP LEU MET LEU ASN ASN LYS SEQRES 15 A 257 SER GLY ASP THR LEU ILE LYS ASP GLY VAL PRO LYS ASP SEQRES 16 A 257 TYR LYS VAL ALA ASP LYS SER GLY GLN ALA ILE THR TYR SEQRES 17 A 257 ALA SER ARG ASN ASP VAL ALA PHE VAL TYR PRO LYS GLY SEQRES 18 A 257 GLN SER GLU PRO ILE VAL LEU VAL ILE PHE THR ASN LYS SEQRES 19 A 257 ASP ASN LYS SER ASP LYS PRO ASN ASP LYS LEU ILE SER SEQRES 20 A 257 GLU THR ALA LYS SER VAL MET LYS GLU PHE FORMUL 2 HOH *161(H2 O) HELIX 1 1 LEU A 33 TYR A 40 1 8 HELIX 2 2 ALA A 69 GLN A 83 5 15 HELIX 3 3 TYR A 88 LYS A 90 5 3 HELIX 4 4 LEU A 109 TYR A 112 5 4 HELIX 5 5 LEU A 119 TYR A 129 1 11 HELIX 6 6 ASN A 132 ILE A 142 1 11 HELIX 7 7 ILE A 145 LEU A 155 1 11 HELIX 8 8 GLU A 168 ASN A 170 5 3 HELIX 9 9 PRO A 183 LEU A 193 1 11 HELIX 10 10 LYS A 201 ASN A 213 1 13 HELIX 11 11 LYS A 215 GLY A 217 5 3 HELIX 12 12 ILE A 221 GLY A 224 1 4 HELIX 13 13 ASP A 276 LYS A 288 1 13 SHEET 1 A 5 LYS A 55 PHE A 60 0 SHEET 2 A 5 HIS A 43 ASP A 50 -1 N ASP A 50 O LYS A 55 SHEET 3 A 5 ILE A 259 ASN A 266 -1 N ASN A 266 O HIS A 43 SHEET 4 A 5 ARG A 244 TYR A 251 -1 N VAL A 250 O ILE A 259 SHEET 5 A 5 LYS A 230 GLN A 237 -1 N GLY A 236 O ASN A 245 SHEET 1 B 2 ARG A 65 ALA A 67 0 SHEET 2 B 2 THR A 180 THR A 182 -1 N SER A 181 O PHE A 66 SHEET 1 C 2 LYS A 94 HIS A 96 0 SHEET 2 C 2 ASP A 116 THR A 118 -1 N ILE A 117 O VAL A 95 CISPEP 1 GLU A 166 ILE A 167 0 0.95 CRYST1 53.700 93.300 138.300 90.00 90.00 90.00 I 2 2 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 0.018622 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007231 0.00000