HEADER HYDROLASE 11-JUN-23 8PCI TITLE STRUCTURE OF SERINE-BETA-LACTAMASE CTX-M-14 FOLLOWING THE TIME- TITLE 2 RESOLVED ACTIVE SITE BINDING OF BORIC ACID, 5000 MS 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 CATALYTIC ACTIVITY, BETA-LACTAMASE ACTIVITY, HYDROLASE ACTIVITY, KEYWDS 2 INHIBITOR, TIME-RESOLVED, TAPE DRIVE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.PRESTER,M.PERBANDT,M.GALCHENKOVA,D.OBERTHUER,O.YEFANOV,W.HINRICHS, AUTHOR 2 H.ROHDE,C.BETZEL REVDAT 3 06-NOV-24 8PCI 1 REMARK REVDAT 2 17-JUL-24 8PCI 1 JRNL REVDAT 1 26-JUN-24 8PCI 0 JRNL AUTH A.PRESTER,M.PERBANDT,M.GALCHENKOVA,D.OBERTHUER,N.WERNER, JRNL AUTH 2 A.HENKEL,J.MARACKE,O.YEFANOV,J.HAKANPAA,G.POMPIDOR,J.MEYER, JRNL AUTH 3 H.CHAPMAN,M.AEPFELBACHER,W.HINRICHS,H.ROHDE,C.BETZEL JRNL TITL TIME-RESOLVED CRYSTALLOGRAPHY OF BORIC ACID BINDING TO THE JRNL TITL 2 ACTIVE SITE SERINE OF THE BETA-LACTAMASE CTX-M-14 AND JRNL TITL 3 SUBSEQUENT 1,2-DIOL ESTERIFICATION. JRNL REF COMMUN CHEM V. 7 152 2024 JRNL REFN ESSN 2399-3669 JRNL PMID 38969718 JRNL DOI 10.1038/S42004-024-01236-W REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 39351 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.810 REMARK 3 FREE R VALUE TEST SET COUNT : 2285 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 38.8800 - 3.7800 0.99 2554 161 0.1250 0.1328 REMARK 3 2 3.7800 - 3.0000 1.00 2391 145 0.1283 0.1479 REMARK 3 3 3.0000 - 2.6200 1.00 2362 147 0.1428 0.1662 REMARK 3 4 2.6200 - 2.3800 1.00 2377 150 0.1374 0.1556 REMARK 3 5 2.3800 - 2.2100 1.00 2303 143 0.1279 0.1587 REMARK 3 6 2.2100 - 2.0800 1.00 2309 139 0.1221 0.1576 REMARK 3 7 2.0800 - 1.9800 1.00 2315 141 0.1215 0.1525 REMARK 3 8 1.9800 - 1.8900 1.00 2316 144 0.1237 0.1704 REMARK 3 9 1.8900 - 1.8200 1.00 2239 135 0.1307 0.1773 REMARK 3 10 1.8200 - 1.7500 1.00 2311 145 0.1307 0.1513 REMARK 3 11 1.7500 - 1.7000 1.00 2312 139 0.1501 0.1994 REMARK 3 12 1.7000 - 1.6500 1.00 2258 136 0.1687 0.1944 REMARK 3 13 1.6500 - 1.6100 1.00 2248 137 0.2093 0.2261 REMARK 3 14 1.6100 - 1.5700 1.00 2309 146 0.2414 0.2577 REMARK 3 15 1.5700 - 1.5300 1.00 2250 138 0.3001 0.3289 REMARK 3 16 1.5300 - 1.5000 0.98 2212 139 0.3860 0.3852 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.057 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.46 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 : 0.017 2086 REMARK 3 ANGLE : 1.409 2860 REMARK 3 CHIRALITY : 0.080 336 REMARK 3 PLANARITY : 0.011 379 REMARK 3 DIHEDRAL : 13.551 783 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 8PCI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : NULL 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 EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40899 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 38.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5842. REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 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 155.52000 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 77.76000 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 77.76000 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 155.52000 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 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 GLN A 25 REMARK 465 THR A 26 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 444 O HOH A 553 2.06 REMARK 500 OE2 GLU A 201 O HOH A 401 2.13 REMARK 500 O HOH A 534 O HOH A 541 2.15 REMARK 500 O4 SO4 A 302 O HOH A 402 2.17 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 -139.77 49.54 REMARK 500 VAL A 103 -135.79 -114.74 REMARK 500 ASN A 106 57.32 -141.57 REMARK 500 SER A 220 -129.74 -105.07 REMARK 500 ARG A 255 143.67 175.62 REMARK 500 GLU A 287 97.63 -66.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 8PCI A 25 289 UNP D2D9A0 D2D9A0_KLEPN 21 283 SEQRES 1 A 263 GLN THR SER ALA VAL GLN GLN LYS LEU ALA ALA LEU GLU SEQRES 2 A 263 LYS SER SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASP SEQRES 3 A 263 THR ALA ASP ASN THR GLN VAL LEU TYR ARG GLY ASP GLU SEQRES 4 A 263 ARG PHE PRO MET CYS SER THR SER LYS VAL MET ALA ALA SEQRES 5 A 263 ALA ALA VAL LEU LYS GLN SER GLU THR GLN LYS GLN LEU SEQRES 6 A 263 LEU ASN GLN PRO VAL GLU ILE LYS PRO ALA ASP LEU VAL SEQRES 7 A 263 ASN TYR ASN PRO ILE ALA GLU LYS HIS VAL ASN GLY THR SEQRES 8 A 263 MET THR LEU ALA GLU LEU SER ALA ALA ALA LEU GLN TYR SEQRES 9 A 263 SER ASP ASN THR ALA MET ASN LYS LEU ILE ALA GLN LEU SEQRES 10 A 263 GLY GLY PRO GLY GLY VAL THR ALA PHE ALA ARG ALA ILE SEQRES 11 A 263 GLY ASP GLU THR PHE ARG LEU ASP ARG THR GLU PRO THR SEQRES 12 A 263 LEU ASN THR ALA ILE PRO GLY ASP PRO ARG ASP THR THR SEQRES 13 A 263 THR PRO ARG ALA MET ALA GLN THR LEU ARG GLN LEU THR SEQRES 14 A 263 LEU GLY HIS ALA LEU GLY GLU THR GLN ARG ALA GLN LEU SEQRES 15 A 263 VAL THR TRP LEU LYS GLY ASN THR THR GLY ALA ALA SER SEQRES 16 A 263 ILE ARG ALA GLY LEU PRO THR SER TRP THR VAL GLY ASP SEQRES 17 A 263 LYS THR GLY SER GLY ASP TYR GLY THR THR ASN ASP ILE SEQRES 18 A 263 ALA VAL ILE TRP PRO GLN GLY ARG ALA PRO LEU VAL LEU SEQRES 19 A 263 VAL THR TYR PHE THR GLN PRO GLN GLN ASN ALA GLU SER SEQRES 20 A 263 ARG ARG ASP VAL LEU ALA SER ALA ALA ARG ILE ILE ALA SEQRES 21 A 263 GLU GLY LEU HET BO4 A 301 7 HET SO4 A 302 10 HETNAM BO4 BORATE ION HETNAM SO4 SULFATE ION FORMUL 2 BO4 B H4 O4 1- FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *164(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 GLU A 287 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 LEU A 48 O VAL A 57 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 LINK OG SER A 70 B BBO4 A 301 1555 1555 1.42 CISPEP 1 GLU A 166 PRO A 167 0 7.41 CRYST1 41.840 41.840 233.280 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 0.023901 0.013799 0.000000 0.00000 SCALE2 0.000000 0.027598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004287 0.00000