HEADER HYDROLASE 04-NOV-03 1RCJ TITLE CRYSTAL STRUCTURE OF E166A MUTANT OF SHV-1 BETA-LACTAMASE WITH THE TITLE 2 TRANS-ENAMINE INTERMEDIATE OF TAZOBACTAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE SHV-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PIT-2; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLA, SHV1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-LACTAMASE, BETA-LACTAM HYDROLASE, PENICILLINASE, DETERGENT KEYWDS 2 BINDING, INHIBITOR DESIGN, COVALENT INTERMEDIATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PADAYATTI,M.S.HELFAND,M.A.TOTIR,M.P.CAREY,A.M.HUJER,P.R.CAREY, AUTHOR 2 R.A.BONOMO,F.VAN DEN AKKER REVDAT 5 23-AUG-23 1RCJ 1 REMARK REVDAT 4 27-OCT-21 1RCJ 1 REMARK SEQADV LINK REVDAT 3 11-OCT-17 1RCJ 1 REMARK REVDAT 2 24-FEB-09 1RCJ 1 VERSN REVDAT 1 17-FEB-04 1RCJ 0 JRNL AUTH P.S.PADAYATTI,M.S.HELFAND,M.A.TOTIR,M.P.CAREY,A.M.HUJER, JRNL AUTH 2 P.R.CAREY,R.A.BONOMO,F.VAN DEN AKKER JRNL TITL TAZOBACTAM FORMS A STOICHIOMETRIC TRANS-ENAMINE INTERMEDIATE JRNL TITL 2 IN THE E166A VARIANT OF SHV-1 BETA-LACTAMASE: 1.63 A CRYSTAL JRNL TITL 3 STRUCTURE JRNL REF BIOCHEMISTRY V. 43 843 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 14744126 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 28279 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) : 0.147 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1372 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 : 2020 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.44000 REMARK 3 B22 (A**2) : 1.64300 REMARK 3 B33 (A**2) : -1.20300 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) : 0.13 REMARK 3 ESD FROM SIGMAA (A) : 0.04 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) : 0.16 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL ANISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1RCJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-03. REMARK 100 THE DEPOSITION ID IS D_1000020650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28328 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03200 REMARK 200 FOR THE DATA SET : 40.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.08000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1G56 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL WAS SOAKED FOR 20 MINUTES IN REMARK 280 MOTHER LIQUOR CONTAINING 5MM TAZOBACTAM PRIOR TO FLASH FREEZING. REMARK 280 30% PEG 6000, 0.1M HEPES, 0.56MM CYMAL-6, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.92400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.86650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.59650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.86650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.92400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.59650 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 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 MET A 69 -146.58 56.03 REMARK 500 TYR A 105 87.71 73.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MA4 A 401 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MA4 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MA4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBI A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G56 RELATED DB: PDB REMARK 900 STRUCTURE OF SHV-1 BETA-LACTAMASE INHIBITED BY TAZOBACTAM REMARK 900 RELATED ID: 1N9B RELATED DB: PDB REMARK 900 ULTRAHIGH RESOLUTION STRUCTURE OF A CLASS A BETA-LACTAMASE: ON THE REMARK 900 MECHANISM AND SPECIFICITY OF THE EXTENDED-SPECTRUM SHV-2 ENZYME DBREF 1RCJ A 26 292 UNP P14557 BLA1_ECOLI 22 286 SEQADV 1RCJ ALA A 166 UNP P14557 GLU 162 ENGINEERED MUTATION 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 ALA 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 A 400 35 HET MA4 A 401 9 HET TBI A 501 20 HETNAM MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE HETNAM TBI TAZOBACTAM TRANS-ENAMINE INTERMEDIATE FORMUL 2 MA4 2(C24 H44 O11) FORMUL 4 TBI C10 H14 N4 O5 S FORMUL 5 HOH *300(H2 O) 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 MET A 129 1 11 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 182 SER A 196 1 15 HELIX 9 9 SER A 200 ASP A 213 1 14 HELIX 10 10 ALA A 217 LEU A 225 1 9 HELIX 11 11 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 GLU A 48 O LEU A 57 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 N ALA A 248 O VAL A 261 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 O THR A 181 N 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 1555 1555 2.04 LINK OG SER A 70 C7 TBI A 501 1555 1555 1.37 SITE 1 AC1 18 ARG A 93 HIS A 96 ARG A 98 VAL A 224 SITE 2 AC1 18 PRO A 226 ALA A 248 VAL A 261 ILE A 263 SITE 3 AC1 18 ALA A 280 ALA A 284 GLU A 288 HOH A 503 SITE 4 AC1 18 HOH A 538 HOH A 555 HOH A 588 HOH A 610 SITE 5 AC1 18 HOH A 625 HOH A 643 SITE 1 AC2 2 ARG A 244 ILE A 279 SITE 1 AC3 9 MET A 69 SER A 70 TYR A 105 ASN A 132 SITE 2 AC3 9 ASN A 170 GLY A 236 ALA A 237 HOH A 550 SITE 3 AC3 9 HOH A 766 CRYST1 49.848 55.193 83.733 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 0.020061 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018118 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011943 0.00000