HEADER HYDROLASE 30-OCT-00 1G56 OBSLTE 07-SEP-04 1G56 1VM1 TITLE STRUCTURE OF SHV-1 BETA-LACTAMASE INHIBITED BY TAZOBACTAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE SHV-1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 GENE: BLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH10B; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBCSK KEYWDS BETA-LACTAMASE, BETA-LACTAM HYDROLASE, PENICILLINASE, KEYWDS 2 DETERGENT BINDING, INHIBITOR DESIGN EXPDTA X-RAY DIFFRACTION AUTHOR A.P.KUZIN,M.NUKAGA,Y.NUKAGA,A.HUJER,R.A.BONOMO,J.R.KNOX REVDAT 3 07-SEP-04 1G56 1 OBSLTE REVDAT 2 01-APR-03 1G56 1 JRNL REVDAT 1 14-FEB-01 1G56 0 JRNL AUTH A.P.KUZIN,M.NUKAGA,Y.NUKAGA,A.HUJER,R.A.BONOMO, JRNL AUTH 2 J.R.KNOX JRNL TITL INHIBITION OF THE SHV-1 BETA-LACTAMASE BY JRNL TITL 2 SULFONES: CRYSTALLOGRAPHIC OBSERVATION OF TWO JRNL TITL 3 REACTION INTERMEDIATES WITH TAZOBACTAM. JRNL REF BIOCHEMISTRY V. 40 1861 2001 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.P.KUZIN,M.NUKAGA,Y.NUKAGA,A.M.HUJER,R.A.BONOMO, REMARK 1 AUTH 2 J.R.KNOX REMARK 1 TITL STRUCTURE OF THE SHV-1 BETA-LACTAMASE REMARK 1 REF BIOCHEMISTRY V. 38 5720 1999 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 13813 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 + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 727 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2023 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.20 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.016 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1G56 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-2000. REMARK 100 THE RCSB ID CODE IS RCSB012246. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-1999 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : MULTIWIRE REMARK 200 DETECTOR MANUFACTURER : SIEMENS HI-STAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69096 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26000 REMARK 200 FOR SHELL : 2.500 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: 1SHV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG-6000, 50 MM HEPES, 0.56 MM REMARK 280 CYMAL-6, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 24.60000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.60000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.05000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 234 CG LYS A 234 CD -0.107 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 34 CB - CG - CD ANGL. DEV. = 41.4 DEGREES REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 DETERGENT USED IN CRYSTALLIZATION. REMARK 600 REMARK 600 TWO COVALENT REACTION INTERMEDIATES ARE OBSERVED REMARK 600 (TAZ 501 AND AKR 503). AN UNREACTED MOLECULE REMARK 600 OF TAZOBACTAM (TAZ 504) IS OBSERVED ON SURFACE. REMARK 600 REMARK 600 IN THIS ENTRY, ACRYLIC ACID (AKR) WAS USED REMARK 600 TO REPRESENT ONE OF THE COVALENT REACTION REMARK 600 INTERMEDIATES: REMARK 600 REMARK 600 CB = C5 OF TAZOBACTAM (TAZ) REMARK 600 CA = C6 OF TAZOBACTAM (TAZ) REMARK 600 C = C7 OF TAZOBACTAM (TAZ) REMARK 600 O = O8 OF TAZOBACTAM (TAZ) REMARK 600 OXT = O9 IN THE CONTEXT OF THE PRIMARY PUBLICATION REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SHV RELATED DB: PDB REMARK 900 NATIVE ENZYME REMARK 999 REMARK 999 SEQUENCE REMARK 999 WE USE A CONSENSUS NUMBERING IN WHICH 239 AND 253 REMARK 999 ARE NOT USED FOR THIS ENZYME. HERE, 238 AND 240 REMARK 999 ARE LINKED, AS ARE 252 AND 254. DBREF 1G56 A 26 292 GB 4337048 AF124984 22 286 SEQRES 1 A 265 SER PRO GLN PRO LEU GLU GLN ILE LYS LEU SER GLU SER SEQRES 2 A 265 GLN LEU SER GLY ARG VAL GLY MET ILE GLU MET ASP LEU SEQRES 3 A 265 ALA SER GLY ARG THR LEU THR ALA TRP ARG ALA ASP GLU SEQRES 4 A 265 ARG PHE PRO MET MET SER THR PHE LYS VAL VAL LEU CYS SEQRES 5 A 265 GLY ALA VAL LEU ALA ARG VAL ASP ALA GLY ASP GLU GLN SEQRES 6 A 265 LEU GLU ARG LYS ILE HIS TYR ARG GLN GLN ASP LEU VAL SEQRES 7 A 265 ASP TYR SER PRO VAL SER GLU LYS HIS LEU ALA ASP GLY SEQRES 8 A 265 MET THR VAL GLY GLU LEU CYS ALA ALA ALA ILE THR MET SEQRES 9 A 265 SER ASP ASN SER ALA ALA ASN LEU LEU LEU ALA THR VAL SEQRES 10 A 265 GLY GLY PRO ALA GLY LEU THR ALA PHE LEU ARG GLN ILE SEQRES 11 A 265 GLY ASP ASN VAL THR ARG LEU ASP ARG TRP GLU THR GLU SEQRES 12 A 265 LEU ASN GLU ALA LEU PRO GLY ASP ALA ARG ASP THR THR SEQRES 13 A 265 THR PRO ALA SER MET ALA ALA THR LEU ARG LYS LEU LEU SEQRES 14 A 265 THR SER GLN ARG LEU SER ALA ARG SER GLN ARG GLN LEU SEQRES 15 A 265 LEU GLN TRP MET VAL ASP ASP ARG VAL ALA GLY PRO LEU SEQRES 16 A 265 ILE ARG SER VAL LEU PRO ALA GLY TRP PHE ILE ALA ASP SEQRES 17 A 265 LYS THR GLY ALA GLY GLU ARG GLY ALA ARG GLY ILE VAL SEQRES 18 A 265 ALA LEU LEU GLY PRO ASN ASN LYS ALA GLU ARG ILE VAL SEQRES 19 A 265 VAL ILE TYR LEU ARG ASP THR PRO ALA SER MET ALA GLU SEQRES 20 A 265 ARG ASN GLN GLN ILE ALA GLY ILE GLY ALA ALA LEU ILE SEQRES 21 A 265 GLU HIS TRP GLN ARG HET MA4 300 35 HET TAZ A 501 20 HET AKR A 503 5 HET TAZ 504 20 HET MA4 301 7 HETNAM MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE HETNAM TAZ TAZOBACTAM HETNAM AKR ACRYLIC ACID FORMUL 2 MA4 2(C24 H44 O11) FORMUL 3 TAZ 2(C10 H12 N4 O5 S) FORMUL 4 AKR C3 H4 O2 FORMUL 7 HOH *175(H2 O1) HELIX 1 1 GLN A 28 SER A 41 1 14 HELIX 2 2 THR A 71 ALA A 86 1 16 HELIX 3 3 ARG A 98 LEU A 102 5 5 HELIX 4 4 VAL A 108 LEU A 113 5 6 HELIX 5 5 VAL A 119 SER A 130 1 12 HELIX 6 6 ASP A 131 VAL A 142 1 12 HELIX 7 7 GLY A 143 ILE A 155 1 13 HELIX 8 8 THR A 167 GLU A 171 5 5 HELIX 9 9 THR A 182 SER A 196 1 15 HELIX 10 10 SER A 200 ASP A 213 1 14 HELIX 11 11 ALA A 217 LEU A 225 1 9 HELIX 12 12 SER A 271 HIS A 289 1 19 SHEET 1 A 5 THR A 56 TRP A 60 0 SHEET 2 A 5 ARG A 43 ASP A 50 -1 N MET A 46 O TRP A 60 SHEET 3 A 5 ARG A 259 ARG A 266 -1 O ILE A 260 N MET A 49 SHEET 4 A 5 ARG A 244 GLY A 251 -1 O ARG A 244 N LEU A 265 SHEET 5 A 5 PHE A 230 ALA A 237 -1 N PHE A 230 O GLY A 251 SHEET 1 B 2 PHE A 66 PRO A 67 0 SHEET 2 B 2 THR A 180 THR A 181 -1 N THR A 181 O PHE A 66 SHEET 1 C 2 LYS A 94 ILE A 95 0 SHEET 2 C 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 SSBOND 1 CYS A 77 CYS A 123 LINK OG SER A 70 C7 TAZ A 501 LINK OG SER A 130 CB AKR A 503 CISPEP 1 GLU A 166 THR A 167 0 5.63 CRYST1 49.200 56.100 82.500 90.00 90.00 90.00 P 21 21 21 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 0.020325 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012121 0.00000