HEADER PROTEIN BINDING 10-DEC-25 9TKX TITLE CLASS A CTX-M-14 WT AT CRYO SSX COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CTX-M-14 BETA-LACTAMASE; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: KPHS_P301310; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS ANTIBIOTIC, CEPHALOSPORIN, CTX-M 14 CLASS A, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.GORE,E.C.SCHULZ REVDAT 1 21-OCT-26 9TKX 0 JRNL AUTH G.GORE,A.PRESTER,K.BARTELS,D.VON STETTEN,E.C.SCHULZ JRNL TITL CEFDINIR BINDING TO A CLASS A BETA-LACTAMASE REVEALED BY JRNL TITL 2 SERIAL CRYO-CRYSTALLOGRAPHY. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 82 672 2026 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 42158994 JRNL DOI 10.1107/S2059798326003992 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2-4158 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32597 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1612 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 2815 174 0.2066 0.2123 REMARK 3 2 3.6600 - 2.9100 1.00 2666 124 0.2234 0.2600 REMARK 3 3 2.9100 - 2.5400 1.00 2642 116 0.2413 0.2663 REMARK 3 4 2.5400 - 2.3100 1.00 2543 149 0.2382 0.2593 REMARK 3 5 2.3100 - 2.1400 1.00 2592 137 0.2220 0.2341 REMARK 3 6 2.1400 - 2.0200 1.00 2549 117 0.2386 0.2649 REMARK 3 7 2.0200 - 1.9200 1.00 2520 149 0.2267 0.2819 REMARK 3 8 1.9100 - 1.8300 1.00 2560 117 0.2523 0.2987 REMARK 3 9 1.8300 - 1.7600 1.00 2555 115 0.2420 0.3231 REMARK 3 10 1.7600 - 1.7000 1.00 2562 115 0.2654 0.2677 REMARK 3 11 1.7000 - 1.6500 1.00 2490 165 0.2501 0.3407 REMARK 3 12 1.6500 - 1.6000 1.00 2491 134 0.2737 0.3125 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 2177 REMARK 3 ANGLE : 0.869 2996 REMARK 3 CHIRALITY : 0.048 349 REMARK 3 PLANARITY : 0.007 402 REMARK 3 DIHEDRAL : 6.323 332 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 9TKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1292152107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 193 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, 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 EIGER2 X CDTE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32733 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 116.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2268. REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: PHASER 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 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 624 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 32 CG CD OE1 NE2 REMARK 480 LYS A 39 CD CE NZ REMARK 480 THR A 52 CB OG1 CG2 REMARK 480 GLN A 89 CG CD OE1 NE2 REMARK 480 LYS A 98 CD CE NZ REMARK 480 GLU A 271 CG CD OE1 OE2 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 554 O HOH A 566 2.19 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 -138.29 45.84 REMARK 500 VAL A 103 -136.62 -118.50 REMARK 500 ASN A 114 17.13 59.52 REMARK 500 ALA A 152 -54.33 87.89 REMARK 500 HIS A 197 19.33 43.97 REMARK 500 LEU A 211 174.07 -58.73 REMARK 500 LYS A 212 -45.77 69.33 REMARK 500 SER A 220 -124.26 -104.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE A 50 10.14 REMARK 500 ILE A 50 10.28 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9TKX A 28 287 UNP A0A0H3H219_KLEPH DBREF2 9TKX A A0A0H3H219 31 290 SEQRES 1 A 260 SER ALA VAL GLN GLN LYS LEU ALA ALA LEU GLU LYS SER SEQRES 2 A 260 SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASP THR ALA SEQRES 3 A 260 ASP ASN THR GLN VAL LEU TYR ARG GLY ASP GLU ARG PHE SEQRES 4 A 260 PRO MET CYS SER THR SER LYS VAL MET ALA ALA ALA ALA SEQRES 5 A 260 VAL LEU LYS GLN SER GLU THR GLN LYS GLN LEU LEU ASN SEQRES 6 A 260 GLN PRO VAL GLU ILE LYS PRO ALA ASP LEU VAL ASN TYR SEQRES 7 A 260 ASN PRO ILE ALA GLU LYS HIS VAL ASN GLY THR MET THR SEQRES 8 A 260 LEU ALA GLU LEU SER ALA ALA ALA LEU GLN TYR SER ASP SEQRES 9 A 260 ASN THR ALA MET ASN LYS LEU ILE ALA GLN LEU GLY GLY SEQRES 10 A 260 PRO GLY GLY VAL THR ALA PHE ALA ARG ALA ILE GLY ASP SEQRES 11 A 260 GLU THR PHE ARG LEU ASP ARG THR GLU PRO THR LEU ASN SEQRES 12 A 260 THR ALA ILE PRO GLY ASP PRO ARG ASP THR THR THR PRO SEQRES 13 A 260 ARG ALA MET ALA GLN THR LEU ARG GLN LEU THR LEU GLY SEQRES 14 A 260 HIS ALA LEU GLY GLU THR GLN ARG ALA GLN LEU VAL THR SEQRES 15 A 260 TRP LEU LYS GLY ASN THR THR GLY ALA ALA SER ILE ARG SEQRES 16 A 260 ALA GLY LEU PRO THR SER TRP THR VAL GLY ASP LYS THR SEQRES 17 A 260 GLY SER GLY ASP TYR GLY THR THR ASN ASP ILE ALA VAL SEQRES 18 A 260 ILE TRP PRO GLN GLY ARG ALA PRO LEU VAL LEU VAL THR SEQRES 19 A 260 TYR PHE THR GLN PRO GLN GLN ASN ALA GLU SER ARG ARG SEQRES 20 A 260 ASP VAL LEU ALA SER ALA ALA ARG ILE ILE ALA GLU GLY HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *228(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 ALA A 154 1 11 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 LYS A 212 1 13 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 ASP A 51 O THR A 56 SHEET 3 AA1 5 LEU A 257 THR A 264 -1 O THR A 264 N ARG A 44 SHEET 4 AA1 5 THR A 243 TRP A 250 -1 N ILE A 249 O LEU A 257 SHEET 5 AA1 5 THR A 230 SER A 237 -1 N THR A 230 O TRP A 250 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 MET A 117 N VAL A 95 CISPEP 1 GLU A 166 PRO A 167 0 7.55 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 2101 2102 2103 2104 2105 CONECT 2102 2101 CONECT 2103 2101 CONECT 2104 2101 CONECT 2105 2101 MASTER 280 0 1 14 9 0 0 6 2174 1 5 20 END