HEADER HYDROLASE 23-MAY-04 1TDL TITLE STRUCTURE OF SER130GLY SHV-1 BETA-LACTAMASE 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 STR. K-12 SUBSTR. DH10B; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 316385; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH10B; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBC SK KEYWDS CLASS A BETA-LACTAMASE, PENICILLINASE, BETA-LACTAM HYDROLASE, KEYWDS 2 DETERGENT BINDING, DRUG DESIGN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SUN,C.R.BETHEL,R.A.BONOMO,J.R.KNOX REVDAT 5 23-AUG-23 1TDL 1 REMARK REVDAT 4 27-OCT-21 1TDL 1 REMARK SEQADV REVDAT 3 11-OCT-17 1TDL 1 REMARK REVDAT 2 24-FEB-09 1TDL 1 VERSN REVDAT 1 23-NOV-04 1TDL 0 JRNL AUTH T.SUN,C.R.BETHEL,R.A.BONOMO,J.R.KNOX JRNL TITL INHIBITOR-RESISTANT CLASS A BETA-LACTAMASES: CONSEQUENCES OF JRNL TITL 2 THE SER130-TO-GLY MUTATION SEEN IN APO AND TAZOBACTAM JRNL TITL 3 STRUCTURES OF THE SHV-1 VARIANT JRNL REF BIOCHEMISTRY V. 43 14111 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15518561 JRNL DOI 10.1021/BI0487903 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 20611 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) : 0.142 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1001 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE : 0.2416 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 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 : 2022 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 414 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.40 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) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.400 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 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 1TDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-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 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 : DOUBLE-MIRROR FRANKS FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS HI-STAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20676 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : 0.03300 REMARK 200 FOR THE DATA SET : 34.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.06800 REMARK 200 R SYM FOR SHELL (I) : 0.06800 REMARK 200 FOR SHELL : 12.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1TDG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 6000, 50 MM HEPES, 0.56 MM REMARK 280 CYMAL-6 DETERGENT, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 24.80400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.04000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.65050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.04000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.80400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.65050 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 -150.41 58.23 REMARK 500 TYR A 105 88.31 70.80 REMARK 500 VAL A 159 -53.49 -120.99 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 810 REMARK 610 EPE A 900 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 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MA4 A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SHV RELATED DB: PDB REMARK 900 SHV-1 BETA-LACTAMASE (WILDTYPE) REMARK 900 RELATED ID: 1TDG RELATED DB: PDB REMARK 900 COMPLEX OF SER130GLY SHV-1 BETA-LACTAMASE WITH TAZOBACTAM REMARK 900 RELATED ID: 1G56 RELATED DB: PDB REMARK 900 COMPLEX OF SHV-1 WITH TAZOBACTAM REMARK 900 RELATED ID: 1RCJ RELATED DB: PDB REMARK 900 COMPLEX OF GLU166ALA SHV-1 WITH TAZOBACTAM DBREF 1TDL A 26 292 UNP P14557 BLA1_ECOLI 22 286 SEQADV 1TDL GLY A 130 UNP P14557 SER 126 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 GLY 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 A 800 47 HET MA4 A 810 10 HET EPE A 900 5 HETNAM MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 MA4 2(C24 H44 O11) FORMUL 4 EPE C8 H18 N2 O4 S FORMUL 5 HOH *414(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 HIS A 112 5 5 HELIX 5 5 VAL A 119 GLY 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 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 ARG A 244 O 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 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 2.03 CISPEP 1 GLU A 166 THR A 167 0 0.85 SITE 1 AC1 20 ARG A 93 LYS A 94 ILE A 95 HIS A 96 SITE 2 AC1 20 ARG A 98 VAL A 224 PRO A 226 ILE A 231 SITE 3 AC1 20 ILE A 246 ALA A 248 VAL A 261 ILE A 279 SITE 4 AC1 20 ALA A 280 ALA A 284 GLU A 288 HOH A 313 SITE 5 AC1 20 HOH A 360 HOH A 444 HOH A 447 HOH A 619 SITE 1 AC2 3 LEU A 220 ARG A 244 ILE A 279 SITE 1 AC3 6 SER A 70 LYS A 73 GLY A 130 LYS A 234 SITE 2 AC3 6 HOH A 359 HOH A 545 CRYST1 49.608 55.301 84.080 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 0.020158 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011893 0.00000