HEADER HYDROLASE 16-DEC-25 9ZOZ TITLE TOHO-1 BETA-LACTAMASE X-RAY STRUCTURE 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: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BLA CTX-M-56; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS BETA-LACTAMASE CLASS A DOUBLE MUTANT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CARTA,L.COATES REVDAT 1 28-OCT-26 9ZOZ 0 JRNL AUTH C.G.WILLIAMS,S.WANG,V.CARTA,P.S.LANGAN,A.F.THOME,S.A.RAMOS, JRNL AUTH 2 J.B.HOLMES,R.K.GHOSH,K.L.WEISS,G.J.O.BERAN,J.D.HARTMAN, JRNL AUTH 3 L.COATES,C.M.RIENSTRA,L.J.MUELLER JRNL TITL NMR CRYSTALLOGRAPHY REVEALS ACTIVE-SITE PROTONATION STATES JRNL TITL 2 OF TOHO-1 BETA-LACTAMASE IN COMPLEX WITH AVIBACTAM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 123 47123 2026 JRNL REFN ESSN 1091-6490 JRNL PMID 42743273 JRNL DOI 10.1073/PNAS.2616547123 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 873 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 22.0600 - 3.6300 1.00 2834 141 0.1573 0.1995 REMARK 3 2 3.6300 - 2.8800 1.00 2708 142 0.1815 0.2267 REMARK 3 3 2.8800 - 2.5200 1.00 2679 130 0.1998 0.2796 REMARK 3 4 2.5200 - 2.2900 1.00 2654 145 0.1970 0.2526 REMARK 3 5 2.2900 - 2.1300 1.00 2641 148 0.2022 0.2532 REMARK 3 6 2.1300 - 2.0000 1.00 2600 167 0.2015 0.2732 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) : 0.184 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.30 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 : 0.006 1994 REMARK 3 ANGLE : 0.808 2708 REMARK 3 CHIRALITY : 0.051 321 REMARK 3 PLANARITY : 0.008 352 REMARK 3 DIHEDRAL : 5.880 275 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 9ZOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000293511. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER IMUS 3.0 MICROFOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17043 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 24.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.15800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.69200 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 (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALIZATIONS WERE PREPARED IN BATCH REMARK 280 AND SLOWLY COOLED TO 277 K, USING 7 MM SPERMINE AND 15% PEG- REMARK 280 8000. THE BUFFER SYSTEM USED WAS 20 MM MES., PH 6.5, BATCH MODE 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 22.06400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.41450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.67350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.41450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.06400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.67350 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 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 -139.00 47.31 REMARK 500 VAL A 103 -126.00 -119.75 REMARK 500 SER A 220 -126.60 -104.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 9ZOZ A 28 290 UNP A3FFV8 A3FFV8_ECOLX 32 291 SEQADV 9ZOZ ASN A 276 UNP A3FFV8 ARG 277 CONFLICT SEQRES 1 A 260 SER VAL GLN GLN GLN LEU GLU ALA LEU GLU LYS SER SER SEQRES 2 A 260 GLY GLY ARG LEU GLY VAL ALA LEU ILE ASN THR ALA ASP SEQRES 3 A 260 ASN SER GLN ILE LEU TYR ARG ALA ASP GLU ARG PHE ALA SEQRES 4 A 260 MET CYS SER THR SER LYS VAL MET ALA ALA ALA ALA VAL SEQRES 5 A 260 LEU LYS GLN SER GLU SER ASP LYS HIS LEU LEU ASN GLN SEQRES 6 A 260 ARG VAL GLU ILE LYS LYS SER ASP LEU VAL ASN TYR ASN SEQRES 7 A 260 PRO ILE ALA GLU LYS HIS VAL ASN GLY THR MET THR LEU SEQRES 8 A 260 ALA GLU LEU GLY ALA ALA ALA LEU GLN TYR SER ASP ASN SEQRES 9 A 260 THR ALA MET ASN LYS LEU ILE ALA HIS LEU GLY GLY PRO SEQRES 10 A 260 ASP LYS VAL THR ALA PHE ALA ARG SER LEU GLY ASP GLU SEQRES 11 A 260 THR PHE ARG LEU ASP ARG THR GLU PRO THR LEU ASN THR SEQRES 12 A 260 ALA ILE PRO GLY ASP PRO ARG ASP THR THR THR PRO LEU SEQRES 13 A 260 ALA MET ALA GLN THR LEU LYS ASN LEU THR LEU GLY LYS SEQRES 14 A 260 ALA LEU ALA GLU THR GLN ARG ALA GLN LEU VAL THR TRP SEQRES 15 A 260 LEU LYS GLY ASN THR THR GLY SER ALA SER ILE ARG ALA SEQRES 16 A 260 GLY LEU PRO LYS SER TRP VAL VAL GLY ASP LYS THR GLY SEQRES 17 A 260 SER GLY ASP TYR GLY THR THR ASN ASP ILE ALA VAL ILE SEQRES 18 A 260 TRP PRO GLU ASN HIS ALA PRO LEU VAL LEU VAL THR TYR SEQRES 19 A 260 PHE THR GLN PRO GLU GLN LYS ALA GLU ASN ARG ASN ASP SEQRES 20 A 260 ILE LEU ALA ALA ALA ALA LYS ILE VAL THR HIS GLY PHE FORMUL 2 HOH *298(H2 O) HELIX 1 AA1 SER A 28 SER A 40 1 13 HELIX 2 AA2 CYS A 69 THR A 71 5 3 HELIX 3 AA3 SER A 72 GLU A 85 1 14 HELIX 4 AA4 HIS A 89 ASN A 92 5 4 HELIX 5 AA5 LYS A 98 LEU A 102 5 5 HELIX 6 AA6 ILE A 108 HIS A 112 5 5 HELIX 7 AA7 LEU A 119 SER A 130 1 12 HELIX 8 AA8 ASP A 131 GLY A 143 1 13 HELIX 9 AA9 GLY A 144 LEU A 155 1 12 HELIX 10 AB1 PRO A 167 THR A 171 5 5 HELIX 11 AB2 THR A 182 GLY A 196 1 15 HELIX 12 AB3 ALA A 200 GLY A 213 1 14 HELIX 13 AB4 SER A 220 LEU A 225 5 6 HELIX 14 AB5 ARG A 275 HIS A 288 1 14 SHEET 1 AA1 5 GLN A 56 TYR A 60 0 SHEET 2 AA1 5 ARG A 43 ASN A 50 -1 N VAL A 46 O TYR A 60 SHEET 3 AA1 5 LEU A 259 THR A 266 -1 O THR A 266 N ARG A 43 SHEET 4 AA1 5 THR A 243 TRP A 251 -1 N ILE A 250 O LEU A 259 SHEET 5 AA1 5 VAL A 230 GLY A 238 -1 N GLY A 236 O ASN A 245 SHEET 1 AA2 2 PHE A 66 ALA 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 ARG 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 2.84 CRYST1 44.128 73.347 74.829 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 0.022661 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013364 0.00000 MASTER 213 0 0 14 9 0 0 6 2262 1 0 20 END