HEADER HYDROLASE 29-APR-22 7ZPV TITLE ROOM TEMPERATURE SSX CRYSTAL STRUCTURE OF CTX-M-14 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: CTX-M-14; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-LACTAMASE, SERIAL CRYSTALLOGRAPHY, SSX, TAPEDRIVE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.OBERTHUER,M.PERBANDT,A.PRESTER,H.ROHDE,C.BETZEL,O.YEFANOV REVDAT 3 03-APR-24 7ZPV 1 JRNL REVDAT 2 31-JAN-24 7ZPV 1 REMARK REVDAT 1 16-NOV-22 7ZPV 0 JRNL AUTH K.A.ZIELINSKI,A.PRESTER,H.ANDALEEB,S.BUI,O.YEFANOV, JRNL AUTH 2 L.CATAPANO,A.HENKEL,M.O.WIEDORN,O.LORBEER,E.CROSAS,J.MEYER, JRNL AUTH 3 V.MARIANI,M.DOMARACKY,T.A.WHITE,H.FLECKENSTEIN,I.SARROU, JRNL AUTH 4 N.WERNER,C.BETZEL,H.ROHDE,M.AEPFELBACHER,H.N.CHAPMAN, JRNL AUTH 5 M.PERBANDT,R.A.STEINER,D.OBERTHUER JRNL TITL RAPID AND EFFICIENT ROOM-TEMPERATURE SERIAL SYNCHROTRON JRNL TITL 2 CRYSTALLOGRAPHY USING THE CFEL TAPEDRIVE. JRNL REF IUCRJ V. 9 778 2022 JRNL REFN ESSN 2052-2525 JRNL PMID 36381150 JRNL DOI 10.1107/S2052252522010193 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49225 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.26 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 : 0.009 2083 REMARK 3 ANGLE : 1.006 2851 REMARK 3 CHIRALITY : 0.071 333 REMARK 3 PLANARITY : 0.007 379 REMARK 3 DIHEDRAL : 17.233 775 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 7ZPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 295 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, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49225 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 17.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2217. REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1400. REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6GTH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% CTX-M-14 SOLUTION (22 MG/ML) WAS REMARK 280 MIXED 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 156.23333 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 78.11667 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 78.11667 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 156.23333 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 TOTAL BURIED SURFACE AREA: 310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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: 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 H HIS A 197 O HOH A 401 1.33 REMARK 500 O HOH A 494 O HOH A 540 1.75 REMARK 500 O HOH A 467 O HOH A 519 2.02 REMARK 500 N HIS A 197 O HOH A 401 2.11 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 412 O HOH A 520 1545 1.97 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 -137.31 47.37 REMARK 500 VAL A 103 -137.47 -110.29 REMARK 500 SER A 220 -128.78 -105.76 REMARK 500 ARG A 255 146.90 -172.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 7ZPV A 27 289 UNP D2D9A0 D2D9A0_KLEPN 23 283 SEQRES 1 A 261 SER ALA VAL GLN GLN LYS LEU ALA ALA LEU GLU LYS SER SEQRES 2 A 261 SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASP THR ALA SEQRES 3 A 261 ASP ASN THR GLN VAL LEU TYR ARG GLY ASP GLU ARG PHE SEQRES 4 A 261 PRO MET CYS SER THR SER LYS VAL MET ALA ALA ALA ALA SEQRES 5 A 261 VAL LEU LYS GLN SER GLU THR GLN LYS GLN LEU LEU ASN SEQRES 6 A 261 GLN PRO VAL GLU ILE LYS PRO ALA ASP LEU VAL ASN TYR SEQRES 7 A 261 ASN PRO ILE ALA GLU LYS HIS VAL ASN GLY THR MET THR SEQRES 8 A 261 LEU ALA GLU LEU SER ALA ALA ALA LEU GLN TYR SER ASP SEQRES 9 A 261 ASN THR ALA MET ASN LYS LEU ILE ALA GLN LEU GLY GLY SEQRES 10 A 261 PRO GLY GLY VAL THR ALA PHE ALA ARG ALA ILE GLY ASP SEQRES 11 A 261 GLU THR PHE ARG LEU ASP ARG THR GLU PRO THR LEU ASN SEQRES 12 A 261 THR ALA ILE PRO GLY ASP PRO ARG ASP THR THR THR PRO SEQRES 13 A 261 ARG ALA MET ALA GLN THR LEU ARG GLN LEU THR LEU GLY SEQRES 14 A 261 HIS ALA LEU GLY GLU THR GLN ARG ALA GLN LEU VAL THR SEQRES 15 A 261 TRP LEU LYS GLY ASN THR THR GLY ALA ALA SER ILE ARG SEQRES 16 A 261 ALA GLY LEU PRO THR SER TRP THR VAL GLY ASP LYS THR SEQRES 17 A 261 GLY SER GLY ASP TYR GLY THR THR ASN ASP ILE ALA VAL SEQRES 18 A 261 ILE TRP PRO GLN GLY ARG ALA PRO LEU VAL LEU VAL THR SEQRES 19 A 261 TYR PHE THR GLN PRO GLN GLN ASN ALA GLU SER ARG ARG SEQRES 20 A 261 ASP VAL LEU ALA SER ALA ALA ARG ILE ILE ALA GLU GLY SEQRES 21 A 261 LEU HET SO4 A 301 5 HET SO4 A 302 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *154(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 274 GLY A 288 1 15 SHEET 1 AA1 5 THR A 55 TYR A 60 0 SHEET 2 AA1 5 ARG A 43 ASP A 50 -1 N VAL A 46 O TYR A 60 SHEET 3 AA1 5 LEU A 258 THR A 265 -1 O TYR A 263 N GLY A 45 SHEET 4 AA1 5 THR A 243 TRP A 251 -1 N ILE A 250 O LEU A 258 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 5.78 CRYST1 42.160 42.160 234.350 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 0.023719 0.013694 0.000000 0.00000 SCALE2 0.000000 0.027389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004267 0.00000