HEADER HYDROLASE 22-JUL-24 9G7Z TITLE CTX-M-14 APO SERIAL CRYSTALLOGRAPHY TEMPERATURE SERIES; 50C, 323K 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 OTHER_DETAILS: RESIDUE 1- 27 SIGNAL PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLACTX-M-14, BLA_2, SAMEA3512100_05103; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CATALYTIC ACTIVITY, BETA-LACTAMASE ACTIVITY, HYDROLASE ACTIVITY, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.PRESTER,D.VON STETTEN,P.MEHRABI,E.C.SCHULZ REVDAT 1 30-JUL-25 9G7Z 0 JRNL AUTH E.C.SCHULZ,A.PRESTER,D.VON STETTEN,G.GORE,C.E.HATTON, JRNL AUTH 2 K.BARTELS,J.P.LEIMKOHL,H.SCHIKORA,H.M.GINN,F.TELLKAMP, JRNL AUTH 3 P.MEHRABI JRNL TITL PROBING THE MODULATION OF ENZYME KINETICS BY JRNL TITL 2 MULTI-TEMPERATURE, TIME-RESOLVED SERIAL CRYSTALLOGRAPHY. JRNL REF NAT COMMUN V. 16 6553 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40670369 JRNL DOI 10.1038/S41467-025-61631-2 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 27322 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1353 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 77.6200 - 3.6600 1.00 2844 145 0.1314 0.1403 REMARK 3 2 3.6600 - 2.9100 1.00 2645 147 0.1513 0.1708 REMARK 3 3 2.9100 - 2.5400 1.00 2630 132 0.1589 0.1978 REMARK 3 4 2.5400 - 2.3100 1.00 2546 147 0.1636 0.1922 REMARK 3 5 2.3100 - 2.1400 1.00 2623 105 0.1575 0.1983 REMARK 3 6 2.1400 - 2.0200 1.00 2504 167 0.1619 0.1877 REMARK 3 7 2.0200 - 1.9100 1.00 2562 116 0.1652 0.2320 REMARK 3 8 1.9100 - 1.8300 1.00 2519 161 0.2208 0.3151 REMARK 3 9 1.8300 - 1.7600 1.00 2539 122 0.3190 0.3747 REMARK 3 10 1.7600 - 1.7000 0.99 2557 111 0.3133 0.2915 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.267 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.46 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 : 0.005 2084 REMARK 3 ANGLE : 0.795 2859 REMARK 3 CHIRALITY : 0.047 337 REMARK 3 PLANARITY : 0.007 381 REMARK 3 DIHEDRAL : 12.450 780 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -5.5142 1.7263 19.6836 REMARK 3 T TENSOR REMARK 3 T11: 0.2226 T22: 0.1811 REMARK 3 T33: 0.2069 T12: 0.0320 REMARK 3 T13: 0.0051 T23: 0.0234 REMARK 3 L TENSOR REMARK 3 L11: 0.6537 L22: 1.3120 REMARK 3 L33: 2.2124 L12: 0.0856 REMARK 3 L13: 0.0375 L23: 0.7202 REMARK 3 S TENSOR REMARK 3 S11: 0.0153 S12: 0.0270 S13: 0.0222 REMARK 3 S21: -0.1749 S22: 0.0088 S23: -0.0020 REMARK 3 S31: -0.2346 S32: -0.1743 S33: -0.0022 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 9G7Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292139293. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-24 REMARK 200 TEMPERATURE (KELVIN) : 323 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.10.2 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL 0.10.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 77.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 244.2 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 148.3 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CTX-M-14 SOLUTION (22 MG/ML) WAS MIXED REMARK 280 WITH 45% PRECIPITANT SOLUTION (40% PEG8000, 200MM LITHIUM REMARK 280 SULFATE, 100MM SODIUM ACETATE, PH 4.5) AND WITH 5% UNDILUTED REMARK 280 SEED STOCK IN BATCH CRYSTALLIZATION SETUPS, BATCH MODE, REMARK 280 TEMPERATURE 293K 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 155.23333 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 77.61667 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 77.61667 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 155.23333 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 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 MET A -2 REMARK 465 VAL A -1 REMARK 465 THR A 0 REMARK 465 LYS A 1 REMARK 465 ARG A 2 REMARK 465 VAL A 3 REMARK 465 GLN A 4 REMARK 465 ARG A 5 REMARK 465 MET A 6 REMARK 465 MET A 7 REMARK 465 PHE A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 ALA A 11 REMARK 465 ALA A 12 REMARK 465 CYS A 13 REMARK 465 ILE A 14 REMARK 465 PRO A 15 REMARK 465 LEU A 16 REMARK 465 LEU A 17 REMARK 465 LEU A 18 REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 ALA A 21 REMARK 465 PRO A 22 REMARK 465 LEU A 23 REMARK 465 TYR A 24 REMARK 465 ALA A 25 REMARK 465 GLN A 26 REMARK 465 THR A 27 REMARK 465 LEU A 288 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 -136.01 44.38 REMARK 500 VAL A 103 -136.31 -111.90 REMARK 500 SER A 220 -122.57 -104.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 9G7Z A -2 288 UNP Q7BGE9 Q7BGE9_KLEPN 1 291 SEQRES 1 A 291 MET VAL THR LYS ARG VAL GLN ARG MET MET PHE ALA ALA SEQRES 2 A 291 ALA ALA CYS ILE PRO LEU LEU LEU GLY SER ALA PRO LEU SEQRES 3 A 291 TYR ALA GLN THR SER ALA VAL GLN GLN LYS LEU ALA ALA SEQRES 4 A 291 LEU GLU LYS SER SER GLY GLY ARG LEU GLY VAL ALA LEU SEQRES 5 A 291 ILE ASP THR ALA ASP ASN THR GLN VAL LEU TYR ARG GLY SEQRES 6 A 291 ASP GLU ARG PHE PRO MET CYS SER THR SER LYS VAL MET SEQRES 7 A 291 ALA ALA ALA ALA VAL LEU LYS GLN SER GLU THR GLN LYS SEQRES 8 A 291 GLN LEU LEU ASN GLN PRO VAL GLU ILE LYS PRO ALA ASP SEQRES 9 A 291 LEU VAL ASN TYR ASN PRO ILE ALA GLU LYS HIS VAL ASN SEQRES 10 A 291 GLY THR MET THR LEU ALA GLU LEU SER ALA ALA ALA LEU SEQRES 11 A 291 GLN TYR SER ASP ASN THR ALA MET ASN LYS LEU ILE ALA SEQRES 12 A 291 GLN LEU GLY GLY PRO GLY GLY VAL THR ALA PHE ALA ARG SEQRES 13 A 291 ALA ILE GLY ASP GLU THR PHE ARG LEU ASP ARG THR GLU SEQRES 14 A 291 PRO THR LEU ASN THR ALA ILE PRO GLY ASP PRO ARG ASP SEQRES 15 A 291 THR THR THR PRO ARG ALA MET ALA GLN THR LEU ARG GLN SEQRES 16 A 291 LEU THR LEU GLY HIS ALA LEU GLY GLU THR GLN ARG ALA SEQRES 17 A 291 GLN LEU VAL THR TRP LEU LYS GLY ASN THR THR GLY ALA SEQRES 18 A 291 ALA SER ILE ARG ALA GLY LEU PRO THR SER TRP THR VAL SEQRES 19 A 291 GLY ASP LYS THR GLY SER GLY ASP TYR GLY THR THR ASN SEQRES 20 A 291 ASP ILE ALA VAL ILE TRP PRO GLN GLY ARG ALA PRO LEU SEQRES 21 A 291 VAL LEU VAL THR TYR PHE THR GLN PRO GLN GLN ASN ALA SEQRES 22 A 291 GLU SER ARG ARG ASP VAL LEU ALA SER ALA ALA ARG ILE SEQRES 23 A 291 ILE ALA GLU GLY LEU HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *135(H2 O) HELIX 1 AA1 SER A 28 GLY A 42 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 SER A 130 1 12 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 273 GLY A 287 1 15 SHEET 1 AA1 5 THR A 56 TYR A 60 0 SHEET 2 AA1 5 ARG A 44 ASP A 51 -1 N VAL A 47 O TYR A 60 SHEET 3 AA1 5 LEU A 257 THR A 264 -1 O TYR A 262 N GLY A 46 SHEET 4 AA1 5 THR A 242 TRP A 250 -1 N ILE A 249 O LEU A 257 SHEET 5 AA1 5 THR A 230 GLY A 238 -1 N GLY A 236 O ASN A 244 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 4.02 CRYST1 41.850 41.850 232.850 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 0.023895 0.013796 0.000000 0.00000 SCALE2 0.000000 0.027591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004295 0.00000 CONECT 2038 2039 2040 2041 2042 CONECT 2039 2038 CONECT 2040 2038 CONECT 2041 2038 CONECT 2042 2038 MASTER 282 0 1 14 9 0 0 6 2080 1 5 23 END