HEADER HYDROLASE/HYDROLASE INHIBITOR 09-JUL-19 6PQC TITLE STRUCTURE OF CEFOTAXIME-CDD-1 BETA-LACTAMASE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE; SOURCE 3 ORGANISM_TAXID: 1496; SOURCE 4 GENE: BLAR1_1, BGU81_18485, SAMEA3374989_01677; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-LACTAMASE, CLASS D, GRAM-POSITIVE, CEFOTAXIME, HYDROLASE, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SMITH,S.B.VAKULENKO REVDAT 4 11-OCT-23 6PQC 1 REMARK REVDAT 3 25-MAR-20 6PQC 1 JRNL REVDAT 2 04-DEC-19 6PQC 1 JRNL REVDAT 1 09-OCT-19 6PQC 0 JRNL AUTH N.K.STEWART,C.A.SMITH,M.TOTH,A.STASYUK,S.B.VAKULENKO JRNL TITL THE CRYSTAL STRUCTURES OF CDD-1, THE INTRINSIC CLASS D JRNL TITL 2 BETA-LACTAMASE FROM THE PATHOGENIC GRAM-POSITIVE BACTERIUM JRNL TITL 3 CLOSTRIDIOIDES DIFFICILE, AND ITS COMPLEX WITH CEFOTAXIME. JRNL REF J.STRUCT.BIOL. V. 208 07391 2019 JRNL REFN ESSN 1095-8657 JRNL PMID 31550535 JRNL DOI 10.1016/J.JSB.2019.09.008 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.490 REMARK 3 FREE R VALUE TEST SET COUNT : 1062 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 39.0580 - 4.1987 1.00 2474 145 0.1623 0.1896 REMARK 3 2 4.1987 - 3.3332 1.00 2323 142 0.1402 0.2053 REMARK 3 3 3.3332 - 2.9120 1.00 2273 140 0.1776 0.2172 REMARK 3 4 2.9120 - 2.6458 1.00 2261 143 0.1863 0.2245 REMARK 3 5 2.6458 - 2.4562 1.00 2256 121 0.1842 0.2348 REMARK 3 6 2.4562 - 2.3114 1.00 2268 114 0.2052 0.2534 REMARK 3 7 2.3114 - 2.1957 1.00 2243 120 0.2100 0.2872 REMARK 3 8 2.1957 - 2.1001 0.99 2200 137 0.2506 0.3027 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.34 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 59 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.8641 26.8827 -30.5682 REMARK 3 T TENSOR REMARK 3 T11: 0.4093 T22: 0.3780 REMARK 3 T33: 0.3549 T12: -0.0268 REMARK 3 T13: 0.0744 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.8065 L22: 0.4619 REMARK 3 L33: 0.8203 L12: -0.1667 REMARK 3 L13: -0.1255 L23: -0.5529 REMARK 3 S TENSOR REMARK 3 S11: 0.1055 S12: 0.2765 S13: 0.1305 REMARK 3 S21: -0.1686 S22: -0.0635 S23: -0.0199 REMARK 3 S31: -0.0481 S32: -0.0830 S33: 0.0012 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 237 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2887 14.0573 -9.8027 REMARK 3 T TENSOR REMARK 3 T11: 0.2331 T22: 0.2163 REMARK 3 T33: 0.2234 T12: -0.0168 REMARK 3 T13: -0.0068 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.7979 L22: 0.5476 REMARK 3 L33: 1.6125 L12: -0.1861 REMARK 3 L13: -0.1146 L23: 0.2161 REMARK 3 S TENSOR REMARK 3 S11: 0.0484 S12: 0.0663 S13: 0.0292 REMARK 3 S21: 0.0043 S22: -0.0190 S23: -0.0122 REMARK 3 S31: 0.0354 S32: -0.0291 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 238 THROUGH 261 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5596 27.5936 -16.6080 REMARK 3 T TENSOR REMARK 3 T11: 0.3424 T22: 0.3184 REMARK 3 T33: 0.3709 T12: -0.0131 REMARK 3 T13: 0.0255 T23: -0.0253 REMARK 3 L TENSOR REMARK 3 L11: 0.1149 L22: 0.7744 REMARK 3 L33: 0.7842 L12: 0.1717 REMARK 3 L13: -0.2470 L23: -0.0993 REMARK 3 S TENSOR REMARK 3 S11: -0.0385 S12: 0.0727 S13: 0.1151 REMARK 3 S21: -0.1072 S22: -0.0316 S23: -0.1734 REMARK 3 S31: -0.2359 S32: 0.1196 S33: 0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 262 THROUGH 310 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4076 29.0845 -22.2142 REMARK 3 T TENSOR REMARK 3 T11: 0.2918 T22: 0.2717 REMARK 3 T33: 0.3508 T12: 0.0159 REMARK 3 T13: 0.0328 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.1354 L22: 1.5817 REMARK 3 L33: 1.2867 L12: -0.5223 REMARK 3 L13: -0.9655 L23: -0.3440 REMARK 3 S TENSOR REMARK 3 S11: 0.1560 S12: 0.1325 S13: 0.3468 REMARK 3 S21: -0.1297 S22: -0.0104 S23: 0.1291 REMARK 3 S31: -0.3618 S32: -0.0750 S33: 0.0004 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 6PQC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242878. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.195 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19410 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 39.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 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 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6EDM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.0, 3.0 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 3 2 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+1/4,X+3/4,-Z+3/4 REMARK 290 14555 -Y+1/4,-X+1/4,-Z+1/4 REMARK 290 15555 Y+3/4,-X+3/4,Z+1/4 REMARK 290 16555 -Y+3/4,X+1/4,Z+3/4 REMARK 290 17555 X+1/4,Z+3/4,-Y+3/4 REMARK 290 18555 -X+3/4,Z+1/4,Y+3/4 REMARK 290 19555 -X+1/4,-Z+1/4,-Y+1/4 REMARK 290 20555 X+3/4,-Z+3/4,Y+1/4 REMARK 290 21555 Z+1/4,Y+3/4,-X+3/4 REMARK 290 22555 Z+3/4,-Y+3/4,X+1/4 REMARK 290 23555 -Z+3/4,Y+1/4,X+3/4 REMARK 290 24555 -Z+1/4,-Y+1/4,-X+1/4 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 61.75650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.75650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.75650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.75650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 61.75650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.75650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 61.75650 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 61.75650 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 61.75650 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 61.75650 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 61.75650 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 61.75650 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 61.75650 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 61.75650 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 61.75650 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 61.75650 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 61.75650 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 61.75650 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 30.87825 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 92.63475 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 92.63475 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 30.87825 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 30.87825 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 30.87825 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 92.63475 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 92.63475 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 30.87825 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 92.63475 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 30.87825 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 92.63475 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 30.87825 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 92.63475 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 92.63475 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 92.63475 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 30.87825 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 92.63475 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 30.87825 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 30.87825 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 30.87825 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 92.63475 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 92.63475 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 30.87825 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 30.87825 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 92.63475 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 92.63475 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 92.63475 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 92.63475 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 30.87825 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 92.63475 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 30.87825 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 92.63475 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 30.87825 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 30.87825 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 30.87825 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 579 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 593 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 310 CG1 CG2 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 ASN A 83 -136.81 -100.54 REMARK 500 LYS A 84 43.66 -147.03 REMARK 500 ASN A 90 69.83 65.81 REMARK 500 CYS A 101 -138.33 54.61 REMARK 500 ASN A 138 48.84 -88.97 REMARK 500 SER A 202 -141.83 -134.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CEF A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 411 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6EDM RELATED DB: PDB REMARK 900 APO-CDD-1 DBREF1 6PQC A 59 310 UNP A0A160YKM3_CLODI DBREF2 6PQC A A0A160YKM3 59 310 SEQADV 6PQC ALA A 238 UNP A0A160YKM LYS 238 ENGINEERED MUTATION SEQADV 6PQC ALA A 244 UNP A0A160YKM LYS 244 ENGINEERED MUTATION SEQRES 1 A 252 SER VAL ASN ILE VAL ASP TYR SER ASP CYS PHE GLU GLY SEQRES 2 A 252 ILE SER GLY GLY ALA ILE PHE CYS ASN THR LYS ASN LYS SEQRES 3 A 252 GLU TYR ASN ILE TYR ASN LYS GLU LEU ILE GLU THR ARG SEQRES 4 A 252 ARG SER PRO CYS SER THR PHE LYS ILE VAL SER THR LEU SEQRES 5 A 252 ILE GLY LEU GLU LYS GLY VAL ILE ASN SER LYS GLU SER SEQRES 6 A 252 VAL MET GLY TYR ASP GLY THR ASP TYR PRO ASN LYS ASN SEQRES 7 A 252 TRP ASN LYS ASN LEU SER LEU GLU GLU ALA PHE LYS GLU SEQRES 8 A 252 SER CYS VAL TRP TYR TYR LYS LYS LEU ILE ASN LYS VAL SEQRES 9 A 252 ASP ALA LYS SER VAL GLN ASN ILE LEU ASP ASP LEU LYS SEQRES 10 A 252 TYR GLY ASN CYS ASP ILE SER GLU TRP GLU GLY ASP LEU SEQRES 11 A 252 LYS ASN GLY LYS GLY HIS LEU ASN GLY PHE TRP LEU GLU SEQRES 12 A 252 SER SER LEU GLN ILE SER PRO LYS GLU GLN VAL GLN THR SEQRES 13 A 252 MET ALA LYS ILE PHE GLU GLY ASP THR ASN PHE LYS LYS SEQRES 14 A 252 GLU HIS ILE ASN ILE LEU ARG ASP ILE MET ALA ILE ASP SEQRES 15 A 252 VAL ASN ASP ALA ASN ILE ASN VAL TYR GLY LYS THR GLY SEQRES 16 A 252 THR GLY PHE ASP GLU LYS ASN LYS ARG VAL ASP ALA TRP SEQRES 17 A 252 PHE VAL GLY MET LEU GLU ARG GLU GLY ASP THR TYR TYR SEQRES 18 A 252 PHE ALA ILE LYS SER ASP ASP SER ASN LYS GLU ILE THR SEQRES 19 A 252 GLY PRO LYS VAL LYS GLU ILE ALA ILE ASN ILE ILE LYS SEQRES 20 A 252 LYS TYR TYR SER VAL HET CEF A 401 26 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET MES A 409 12 HET MPD A 410 8 HET MPD A 411 8 HETNAM CEF CEFOTAXIME, C3' CLEAVED, OPEN, BOUND FORM HETNAM SO4 SULFATE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 CEF C14 H15 N5 O5 S2 FORMUL 3 SO4 7(O4 S 2-) FORMUL 10 MES C6 H13 N O4 S FORMUL 11 MPD 2(C6 H14 O2) FORMUL 13 HOH *97(H2 O) HELIX 1 AA1 TYR A 65 GLU A 70 5 6 HELIX 2 AA2 ASN A 90 GLU A 95 1 6 HELIX 3 AA3 PRO A 100 THR A 103 5 4 HELIX 4 AA4 PHE A 104 LYS A 115 1 12 HELIX 5 AA5 ASN A 134 ASN A 138 5 5 HELIX 6 AA6 SER A 142 SER A 150 1 9 HELIX 7 AA7 CYS A 151 ASN A 160 1 10 HELIX 8 AA8 ASP A 163 LYS A 175 1 13 HELIX 9 AA9 ASP A 187 GLY A 191 5 5 HELIX 10 AB1 SER A 207 GLU A 220 1 14 HELIX 11 AB2 LYS A 226 MET A 237 1 12 HELIX 12 AB3 THR A 292 TYR A 308 1 17 SHEET 1 AA1 7 VAL A 60 ILE A 62 0 SHEET 2 AA1 7 GLU A 85 TYR A 89 1 O TYR A 86 N ASN A 61 SHEET 3 AA1 7 GLY A 74 ASN A 80 -1 N PHE A 78 O ASN A 87 SHEET 4 AA1 7 ASP A 276 SER A 284 -1 O TYR A 279 N CYS A 79 SHEET 5 AA1 7 ARG A 262 ARG A 273 -1 N LEU A 271 O TYR A 278 SHEET 6 AA1 7 ASN A 247 ASP A 257 -1 N ASP A 257 O ARG A 262 SHEET 7 AA1 7 ALA A 238 ILE A 239 -1 N ILE A 239 O VAL A 248 LINK OG SER A 102 C8 CEF A 401 1555 1555 1.43 SITE 1 AC1 10 CYS A 101 SER A 102 PRO A 133 SER A 150 SITE 2 AC1 10 LYS A 192 LYS A 251 THR A 252 GLY A 253 SITE 3 AC1 10 THR A 254 PRO A 294 SITE 1 AC2 3 LYS A 157 LYS A 161 HOH A 511 SITE 1 AC3 4 ARG A 97 ASN A 178 GLN A 205 SO4 A 408 SITE 1 AC4 2 ARG A 97 ASN A 178 SITE 1 AC5 6 ASN A 119 SER A 123 VAL A 124 ASP A 163 SITE 2 AC5 6 HOH A 532 HOH A 569 SITE 1 AC6 2 LYS A 139 MES A 409 SITE 1 AC7 4 LYS A 226 LYS A 227 HOH A 501 HOH A 571 SITE 1 AC8 4 GLU A 95 THR A 96 ARG A 97 SO4 A 403 SITE 1 AC9 8 LYS A 135 ASN A 138 GLU A 185 LYS A 189 SITE 2 AC9 8 ASN A 190 GLY A 191 GLU A 258 SO4 A 406 SITE 1 AD1 4 GLU A 114 ILE A 170 ASP A 173 ASN A 224 SITE 1 AD2 6 ASP A 128 THR A 130 TYR A 132 HIS A 194 SITE 2 AD2 6 HOH A 543 HOH A 556 CRYST1 123.513 123.513 123.513 90.00 90.00 90.00 P 43 3 2 24 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 0.008096 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008096 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008096 0.00000