HEADER HYDROLASE/ANTIBIOTIC 20-MAY-14 4PM9 TITLE CRYSTAL STRUCTURE OF CTX-M-14 S70G:S237A:R276A BETA-LACTAMASE IN TITLE 2 COMPLEX WITH CEFOTAXIME AT 1.45 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE CTX-M-14; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-291; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1125630; SOURCE 4 STRAIN: HS11286; SOURCE 5 GENE: KPHS_P301310; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CLASS A BETA-LACTAMASE, CEFOTAXIME, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.M.CARDENAS,C.J.ADAMSKI,B.SANKARAN,N.G.BROWN,L.B.HORTON,T.PALZKILL REVDAT 6 27-DEC-23 4PM9 1 REMARK REVDAT 5 30-JUN-21 4PM9 1 COMPND AUTHOR HETNAM REVDAT 4 11-DEC-19 4PM9 1 REMARK REVDAT 3 13-SEP-17 4PM9 1 SOURCE JRNL REMARK REVDAT 2 04-MAR-15 4PM9 1 JRNL REVDAT 1 31-DEC-14 4PM9 0 JRNL AUTH C.J.ADAMSKI,A.M.CARDENAS,N.G.BROWN,L.B.HORTON,B.SANKARAN, JRNL AUTH 2 B.V.PRASAD,H.F.GILBERT,T.PALZKILL JRNL TITL MOLECULAR BASIS FOR THE CATALYTIC SPECIFICITY OF THE CTX-M JRNL TITL 2 EXTENDED-SPECTRUM BETA-LACTAMASES. JRNL REF BIOCHEMISTRY V. 54 447 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 25489790 JRNL DOI 10.1021/BI501195G REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 39269 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1971 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 37.4651 - 3.1319 1.00 3984 232 0.1514 0.1673 REMARK 3 2 3.1319 - 2.4860 0.99 3816 202 0.1728 0.1841 REMARK 3 3 2.4860 - 2.1718 1.00 3768 233 0.1596 0.1747 REMARK 3 4 2.1718 - 1.9733 1.00 3765 198 0.1618 0.1830 REMARK 3 5 1.9733 - 1.8318 0.99 3797 179 0.1606 0.2097 REMARK 3 6 1.8318 - 1.7238 0.99 3699 181 0.1589 0.1699 REMARK 3 7 1.7238 - 1.6375 0.98 3681 195 0.1557 0.1846 REMARK 3 8 1.6375 - 1.5662 0.97 3659 174 0.1557 0.1790 REMARK 3 9 1.5662 - 1.5059 0.96 3604 175 0.1640 0.1973 REMARK 3 10 1.5059 - 1.4540 0.94 3525 202 0.1959 0.2116 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 34.65 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.170 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) : -1.23410 REMARK 3 B22 (A**2) : 0.33090 REMARK 3 B33 (A**2) : 0.90320 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 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 : 0.005 2012 REMARK 3 ANGLE : 1.120 2745 REMARK 3 CHIRALITY : 0.065 324 REMARK 3 PLANARITY : 0.005 361 REMARK 3 DIHEDRAL : 12.951 777 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 4PM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000201667. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41240 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 37.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG 4000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 296K 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 20.76500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.33750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.86850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.33750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.76500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.86850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 CYS A 69 -138.48 45.00 REMARK 500 VAL A 103 -137.03 -113.71 REMARK 500 SER A 220 -128.16 -102.27 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 CE3 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PM5 RELATED DB: PDB REMARK 900 RELATED ID: 4PM6 RELATED DB: PDB REMARK 900 RELATED ID: 4PM7 RELATED DB: PDB REMARK 900 RELATED ID: 4PM8 RELATED DB: PDB REMARK 900 RELATED ID: 4PMA RELATED DB: PDB DBREF 4PM9 A 26 290 UNP G8XD06 G8XD06_KLEPH 30 291 SEQADV 4PM9 GLY A 70 UNP G8XD06 SER 73 ENGINEERED MUTATION SEQADV 4PM9 ALA A 237 UNP G8XD06 SER 240 ENGINEERED MUTATION SEQADV 4PM9 ALA A 276 UNP G8XD06 ARG 277 ENGINEERED MUTATION SEQRES 1 A 262 THR SER ALA VAL GLN GLN LYS LEU ALA ALA LEU GLU LYS SEQRES 2 A 262 SER SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASP THR SEQRES 3 A 262 ALA ASP ASN THR GLN VAL LEU TYR ARG GLY ASP GLU ARG SEQRES 4 A 262 PHE PRO MET CYS GLY THR SER LYS VAL MET ALA ALA ALA SEQRES 5 A 262 ALA VAL LEU LYS GLN SER GLU THR GLN LYS GLN LEU LEU SEQRES 6 A 262 ASN GLN PRO VAL GLU ILE LYS PRO ALA 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 SER ALA ALA ALA LEU GLN TYR SER SEQRES 9 A 262 ASP ASN THR ALA MET ASN LYS LEU ILE ALA GLN LEU GLY SEQRES 10 A 262 GLY PRO GLY GLY VAL THR ALA PHE ALA ARG ALA ILE GLY SEQRES 11 A 262 ASP GLU THR PHE ARG LEU ASP ARG THR GLU 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 ARG ALA MET ALA GLN THR LEU ARG GLN LEU THR LEU SEQRES 14 A 262 GLY HIS ALA LEU GLY GLU THR GLN ARG ALA GLN LEU VAL SEQRES 15 A 262 THR TRP LEU LYS GLY ASN THR THR GLY ALA ALA SER ILE SEQRES 16 A 262 ARG ALA GLY LEU PRO THR SER TRP THR VAL GLY ASP LYS SEQRES 17 A 262 THR GLY ALA GLY ASP TYR GLY THR THR ASN ASP ILE ALA SEQRES 18 A 262 VAL ILE TRP PRO GLN GLY ARG ALA PRO LEU VAL LEU VAL SEQRES 19 A 262 THR TYR PHE THR GLN PRO GLN GLN ASN ALA GLU SER ARG SEQRES 20 A 262 ALA ASP VAL LEU ALA SER ALA ALA ARG ILE ILE ALA GLU SEQRES 21 A 262 GLY LEU HET CE3 A 301 30 HETNAM CE3 (6R,7R)-3-(ACETYLOXYMETHYL)-7-[[(2Z)-2-(2-AMINO-1,3- HETNAM 2 CE3 THIAZOL-4-YL)-2-METHOXYIMINO-ETHANOYL]AMINO]-8-OXO-5- HETNAM 3 CE3 THIA-1-AZABICY CLO[4.2.0]OCT-2-ENE-2-CARBOXYLIC ACID HETSYN CE3 CEFOTAXIME FORMUL 2 CE3 C16 H17 N5 O7 S2 FORMUL 3 HOH *305(H2 O) HELIX 1 AA1 SER A 27 GLY A 41 1 15 HELIX 2 AA2 CYS A 69 THR A 71 5 3 HELIX 3 AA3 SER A 72 SER A 84 1 13 HELIX 4 AA4 GLN A 89 ASN A 92 5 4 HELIX 5 AA5 LYS A 98 LEU A 102 5 5 HELIX 6 AA6 ILE A 108 VAL A 113 5 6 HELIX 7 AA7 LEU A 119 TYR A 129 1 11 HELIX 8 AA8 ASP A 131 LEU A 142 1 12 HELIX 9 AA9 GLY A 144 ILE A 155 1 12 HELIX 10 AB1 PRO A 167 THR A 171 5 5 HELIX 11 AB2 THR A 182 LEU A 195 1 14 HELIX 12 AB3 GLY A 200 GLY A 213 1 14 HELIX 13 AB4 SER A 220 LEU A 225 5 6 HELIX 14 AB5 ARG A 275 GLU A 288 1 14 SHEET 1 AA1 5 THR A 55 TYR A 60 0 SHEET 2 AA1 5 ARG A 43 ASP A 50 -1 N ASP A 50 O THR A 55 SHEET 3 AA1 5 LEU A 259 THR A 266 -1 O TYR A 264 N GLY A 45 SHEET 4 AA1 5 THR A 243 TRP A 251 -1 N ASP A 246 O THR A 263 SHEET 5 AA1 5 THR A 230 GLY A 238 -1 N THR A 230 O TRP A 251 SHEET 1 AA2 2 PHE A 66 PRO A 67 0 SHEET 2 AA2 2 THR A 180 THR A 181 -1 O THR A 181 N PHE A 66 SHEET 1 AA3 2 PRO A 94 ILE A 97 0 SHEET 2 AA3 2 GLY A 115 THR A 118 -1 O GLY A 115 N ILE A 97 CISPEP 1 GLU A 166 PRO A 167 0 5.85 SITE 1 AC1 17 CYS A 69 GLY A 70 ASN A 104 TYR A 105 SITE 2 AC1 17 SER A 130 ASN A 132 PRO A 167 ASN A 170 SITE 3 AC1 17 THR A 216 LYS A 234 THR A 235 GLY A 236 SITE 4 AC1 17 ALA A 237 GLY A 238 HOH A 702 HOH A 704 SITE 5 AC1 17 HOH A 705 CRYST1 41.530 61.737 86.675 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 0.024079 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011537 0.00000