PDB Short entry for 5A93 HEADER HYDROLASE 17-JUL-15 5A93 TITLE 293K JOINT X-RAY NEUTRON WITH CEFOTAXIME: EXPLORING THE MECHANISM OF TITLE 2 BETA-LACTAM RING PROTONATION IN THE CLASS A BETA-LACTAMASE ACYLATION TITLE 3 MECHANISM USING NEUTRON AND X-RAY CRYSTALLOGRAPHY CAVEAT 5A93 CEF A 1291 HAS WRONG CHIRALITY AT ATOM C6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE CTX-M-97; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TOHO1 BETA LACTAMASE; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, JOINT NEUTRON X-RAY, BETA LACTAMASE EXPDTA NEUTRON DIFFRACTION; X-RAY DIFFRACTION AUTHOR V.G.VANDAVASI,K.L.WEISS,J.B.COOPER,P.T.ERSKINE,S.J.TOMANICEK, AUTHOR 2 A.OSTERMANN,T.E.SCHRADER,S.L.GINELL,L.COATES REVDAT 8 10-JAN-24 5A93 1 REMARK LINK REVDAT 7 14-NOV-18 5A93 1 REMARK REVDAT 6 03-OCT-18 5A93 1 CAVEAT COMPND REMARK HET REVDAT 6 2 1 HETNAM HETSYN FORMUL LINK REVDAT 6 3 1 ATOM REVDAT 5 06-JUN-18 5A93 1 REMARK REVDAT 4 14-FEB-18 5A93 1 REMARK REVDAT 3 25-JAN-17 5A93 1 REMARK REVDAT 2 27-JAN-16 5A93 1 JRNL REVDAT 1 16-DEC-15 5A93 0 JRNL AUTH V.G.VANDAVASI,K.L.WEISS,J.B.COOPER,P.T.ERSKINE, JRNL AUTH 2 S.J.TOMANICEK,A.OSTERMANN,T.E.SCHRADER,S.L.GINELL,L.COATES JRNL TITL EXPLORING THE MECHANISM OF BETA-LACTAM RING PROTONATION IN JRNL TITL 2 THE CLASS A BETA-LACTAMASE ACYLATION MECHANISM USING NEUTRON JRNL TITL 3 AND X-RAY CRYSTALLOGRAPHY. JRNL REF J.MED.CHEM. V. 59 474 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 26630115 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01215 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 41055 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.5045 - 3.9313 1.00 2782 134 0.1320 0.1539 REMARK 3 2 3.9313 - 3.1245 1.00 2667 152 0.1252 0.1350 REMARK 3 3 3.1245 - 2.7308 1.00 2604 150 0.1413 0.1586 REMARK 3 4 2.7308 - 2.4817 1.00 2628 138 0.1242 0.1435 REMARK 3 5 2.4817 - 2.3041 1.00 2625 117 0.1261 0.1475 REMARK 3 6 2.3041 - 2.1684 1.00 2616 129 0.1204 0.1403 REMARK 3 7 2.1684 - 2.0599 1.00 2580 138 0.1228 0.1544 REMARK 3 8 2.0599 - 1.9704 1.00 2608 141 0.1254 0.1550 REMARK 3 9 1.9704 - 1.8946 1.00 2548 145 0.1276 0.1505 REMARK 3 10 1.8946 - 1.8292 1.00 2571 154 0.1346 0.1706 REMARK 3 11 1.8292 - 1.7721 1.00 2600 130 0.1441 0.1748 REMARK 3 12 1.7721 - 1.7215 1.00 2589 155 0.1538 0.1899 REMARK 3 13 1.7215 - 1.6762 1.00 2553 125 0.1582 0.1564 REMARK 3 14 1.6762 - 1.6353 1.00 2589 125 0.1668 0.2529 REMARK 3 15 1.6353 - 1.5981 0.95 2429 133 0.1881 0.2198 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.180 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 3 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 72.3 REMARK 3 NUMBER OF REFLECTIONS : 11579 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 574 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 15.0300 - 3.4815 0.92 3609 180 0.1962 0.2150 REMARK 3 2 3.4815 - 2.7690 0.76 2884 177 0.2258 0.2408 REMARK 3 3 2.7690 - 2.4206 0.65 2456 118 0.2343 0.2802 REMARK 3 4 2.4206 - 2.2001 0.55 2056 99 0.2628 0.2537 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.740 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 4259 REMARK 3 ANGLE : 1.248 7738 REMARK 3 CHIRALITY : 0.087 347 REMARK 3 PLANARITY : 0.007 681 REMARK 3 DIHEDRAL : 19.221 1183 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5A93 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1290064387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.9 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 FR-E DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41094 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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 2XR0 REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : NULL REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 6.10 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : MANDI REMARK 230 WAVELENGTH OR RANGE (A) : 3.0 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : MIRRORS REMARK 230 REMARK 230 DETECTOR TYPE : SNS ANGER CAMERA REMARK 230 DETECTOR MANUFACTURER : ORNL ANGER CAMERA REMARK 230 INTENSITY-INTEGRATION SOFTWARE : MANTID, D*TREK REMARK 230 DATA SCALING SOFTWARE : MANTID, D*TREK REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 11803 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 230 RESOLUTION RANGE LOW (A) : 15.210 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 71.4 REMARK 230 DATA REDUNDANCY : 3.900 REMARK 230 R MERGE (I) : 0.17100 REMARK 230 R SYM (I) : 0.17000 REMARK 230 <I/SIGMA(I)> FOR THE DATA SET : 9.4000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 230 COMPLETENESS FOR SHELL (%) : 49.7 REMARK 230 DATA REDUNDANCY IN SHELL : 2.20 REMARK 230 R MERGE FOR SHELL (I) : 0.25200 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : CNS REMARK 230 STARTING MODEL: PDB ENTRY 2XR0 REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.9. PH 6.1 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.91333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.95667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.95667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.91333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 A2011 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2215 LIES ON A SPECIAL POSITION. 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 ALA A 26 REMARK 465 ASN A 27 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2044 O HOH A 2045 2.01 REMARK 500 O HOH A 2165 O HOH A 2171 2.05 REMARK 500 O HOH A 2104 O HOH A 2107 2.05 REMARK 500 OE2 GLU A 96 O HOH A 2073 2.12 REMARK 500 O HOH A 2021 O HOH A 2035 2.12 REMARK 500 O2 SO4 A 1293 O HOH A 2234 2.16 REMARK 500 O HOH A 2182 O HOH A 2184 2.17 REMARK 500 O HOH A 2041 O HOH A 2042 2.17 REMARK 500 OD1 ASP A 146 O HOH A 2104 2.18 REMARK 500 O HOH A 2179 O HOH A 2180 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2028 O HOH A 2184 3455 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 275 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 69 -142.84 51.75 REMARK 500 CYS A 69 -144.91 55.65 REMARK 500 VAL A 103 -136.60 -114.84 REMARK 500 SER A 220 -129.52 -99.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2062 DISTANCE = 5.97 ANGSTROMS 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 1292 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for Ligand PCZ A1291 bound to SER A REMARK 800 70 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A90 RELATED DB: PDB REMARK 900 100K NEUTRON LIGAND FREE: EXPLORING THE MECHANISM OF BETA-LACTAM REMARK 900 RING PROTONATION IN THE CLASS A BETA- LACTAMASE ACYLATION MECHANISM REMARK 900 USING NEUTRON AND X-RAY CRYSTALLOGRAPHY REMARK 900 RELATED ID: 5A91 RELATED DB: PDB REMARK 900 15K X-RAY LIGAND FREE: EXPLORING THE MECHANISM OF BETA-LACTAM RING REMARK 900 PROTONATION IN THE CLASS A BETA- LACTAMASE ACYLATION MECHANISM REMARK 900 USING NEUTRON AND X-RAY CRYSTALLOGRAPHY REMARK 900 RELATED ID: 5A92 RELATED DB: PDB REMARK 900 15K X-RAY STRUCTURE WITH CEFOTAXIME: EXPLORING THE MECHANISM OF REMARK 900 BETA-LACTAM RING PROTONATION IN THE CLASS A BETA-LACTAMASE REMARK 900 ACYLATION MECHANISM USING NEUTRON AND X-RAY CRYSTALLOGRAPHY DBREF 5A93 A 26 290 UNP E1ANH6 BLC97_ECOLX 30 291 SEQADV 5A93 ALA A 166 UNP E1ANH6 GLU 169 ENGINEERED MUTATION SEQADV 5A93 ASN A 274 UNP E1ANH6 SER 275 CONFLICT SEQADV 5A93 ASN A 276 UNP E1ANH6 ARG 277 CONFLICT SEQRES 1 A 262 ALA ASN SER VAL GLN GLN GLN LEU GLU ALA LEU GLU LYS SEQRES 2 A 262 SER SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASN THR SEQRES 3 A 262 ALA ASP ASN SER GLN ILE LEU TYR ARG ALA ASP GLU ARG SEQRES 4 A 262 PHE ALA MET CYS SER THR SER LYS VAL MET ALA ALA ALA SEQRES 5 A 262 ALA VAL LEU LYS GLN SER GLU SER ASP LYS HIS LEU LEU SEQRES 6 A 262 ASN GLN ARG VAL GLU ILE LYS LYS SER ASP LEU VAL ASN SEQRES 7 A 262 TYR ASN PRO ILE ALA GLU LYS HIS VAL ASN GLY THR MET SEQRES 8 A 262 THR LEU ALA GLU LEU GLY ALA ALA ALA LEU GLN TYR SER SEQRES 9 A 262 ASP ASN THR ALA MET ASN LYS LEU ILE ALA HIS LEU GLY SEQRES 10 A 262 GLY PRO ASP LYS VAL THR ALA PHE ALA ARG SER LEU GLY SEQRES 11 A 262 ASP GLU THR PHE ARG LEU ASP ARG THR ALA PRO THR LEU SEQRES 12 A 262 ASN THR ALA ILE PRO GLY ASP PRO ARG ASP THR THR THR SEQRES 13 A 262 PRO LEU ALA MET ALA GLN THR LEU LYS ASN LEU THR LEU SEQRES 14 A 262 GLY LYS ALA LEU ALA GLU THR GLN ARG ALA GLN LEU VAL SEQRES 15 A 262 THR TRP LEU LYS GLY ASN THR THR GLY SER ALA SER ILE SEQRES 16 A 262 ARG ALA GLY LEU PRO LYS SER TRP VAL VAL GLY ASP LYS SEQRES 17 A 262 THR GLY SER GLY ASP TYR GLY THR THR ASN ASP ILE ALA SEQRES 18 A 262 VAL ILE TRP PRO GLU ASN HIS ALA PRO LEU VAL LEU VAL SEQRES 19 A 262 THR TYR PHE THR GLN PRO GLU GLN LYS ALA GLU ASN ARG SEQRES 20 A 262 ASN ASP ILE LEU ALA ALA ALA ALA LYS ILE VAL THR HIS SEQRES 21 A 262 GLY PHE HET CEF A1291 26 HET SO4 A1292 5 HET SO4 A1293 5 HET SO4 A1294 5 HET SO4 A1295 5 HET SO4 A1296 5 HETNAM CEF CEFOTAXIME, C3' CLEAVED, OPEN, BOUND FORM HETNAM SO4 SULFATE ION FORMUL 2 CEF C14 H15 N5 O5 S2 FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *238(H2 O) HELIX 1 1 SER A 28 GLY A 41 1 14 HELIX 2 2 CYS A 69 THR A 71 5 3 HELIX 3 3 SER A 72 GLU A 85 1 14 HELIX 4 4 HIS A 89 ASN A 92 5 4 HELIX 5 5 LYS A 98 LEU A 102 5 5 HELIX 6 6 ILE A 108 VAL A 113 5 6 HELIX 7 7 LEU A 119 TYR A 129 1 11 HELIX 8 8 ASP A 131 GLY A 143 1 13 HELIX 9 9 GLY A 144 LEU A 155 1 12 HELIX 10 10 PRO A 167 THR A 171 5 5 HELIX 11 11 THR A 182 GLY A 196 1 15 HELIX 12 12 ALA A 200 GLY A 213 1 14 HELIX 13 13 SER A 220 LEU A 225 5 6 HELIX 14 14 ARG A 275 THR A 287 1 13 SHEET 1 AA 5 GLN A 56 TYR A 60 0 SHEET 2 AA 5 ARG A 43 ASN A 50 -1 O VAL A 46 N TYR A 60 SHEET 3 AA 5 LEU A 259 THR A 266 -1 O VAL A 260 N ILE A 49 SHEET 4 AA 5 THR A 244 TRP A 251 -1 O THR A 244 N PHE A 265 SHEET 5 AA 5 VAL A 230 SER A 237 -1 O VAL A 230 N TRP A 251 SHEET 1 AB 2 PHE A 66 ALA A 67 0 SHEET 2 AB 2 THR A 180 THR A 181 -1 O THR A 181 N PHE A 66 SHEET 1 AC 2 ARG A 94 GLU A 96 0 SHEET 2 AC 2 THR A 116 THR A 118 -1 O MET A 117 N VAL A 95 LINK OG SER A 70 C8 CEF A1291 1555 1555 1.39 CISPEP 1 ALA A 166 PRO A 167 0 6.30 SITE 1 AC1 7 TRP A 229 PRO A 252 GLU A 254 ASN A 255 SITE 2 AC1 7 HIS A 256 HOH A2232 HOH A2233 SITE 1 AC2 11 LYS A 82 ALA A 198 ASN A 274 ASN A 276 SITE 2 AC2 11 ASP A 277 HOH A2056 HOH A2152 HOH A2224 SITE 3 AC2 11 HOH A2226 HOH A2234 HOH A2235 SITE 1 AC3 4 ALA A 52 ARG A 178 HOH A2143 HOH A2236 SITE 1 AC4 2 HIS A 89 ASN A 92 SITE 1 AC5 7 HIS A 112 PRO A 226 LYS A 227 SER A 228 SITE 2 AC5 7 HOH A2083 HOH A2194 HOH A2238 SITE 1 AC6 17 CYS A 69 SER A 70 ASN A 104 TYR A 105 SITE 2 AC6 17 SER A 130 ASN A 132 PRO A 167 ASN A 170 SITE 3 AC6 17 LYS A 234 THR A 235 GLY A 236 SER A 237 SITE 4 AC6 17 GLY A 238 ASN A 274 HOH A2198 HOH A2200 SITE 5 AC6 17 HOH A2201 CRYST1 73.315 73.315 98.870 90.00 90.00 120.00 P 32 2 1 6 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 0.013640 0.007875 0.000000 0.00000 SCALE2 0.000000 0.015750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010114 0.00000