HEADER HYDROLASE 18-DEC-25 9ZQQ TITLE TOHO1-AVIBACTAM 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, AVIBACTAM PROTEIN-LIGAND COMPLEX, CLASS A, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CARTA,L.COATES REVDAT 1 28-OCT-26 9ZQQ 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) : 23.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18030 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 951 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 23.3300 - 3.8200 1.00 2587 139 0.1687 0.2050 REMARK 3 2 3.8200 - 3.0400 1.00 2457 140 0.1914 0.2407 REMARK 3 3 3.0400 - 2.6500 1.00 2445 119 0.2169 0.2514 REMARK 3 4 2.6500 - 2.4100 1.00 2394 173 0.2160 0.2961 REMARK 3 5 2.4100 - 2.2400 1.00 2404 110 0.2162 0.3038 REMARK 3 6 2.2400 - 2.1100 1.00 2421 119 0.2218 0.2969 REMARK 3 7 2.1100 - 2.0000 1.00 2371 151 0.2433 0.3263 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) : 0.262 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.011 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.07 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 : 0.007 2034 REMARK 3 ANGLE : 0.865 2767 REMARK 3 CHIRALITY : 0.050 327 REMARK 3 PLANARITY : 0.007 357 REMARK 3 DIHEDRAL : 10.545 291 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 9ZQQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000303314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JAN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : 18092 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 24.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 17.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 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) : 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 (%): 46.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM MES PH 6.5, 7MM SPERMINE, 30% PEG REMARK 280 -8K, TOHO-1 CRYSTALS SOAKED WITH 7MM AVIBACTAM CRYSTALLIZATION REMARK 280 BUFFER, BATCH MODE, TEMPERATURE 277K 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 22.41700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.19550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.64750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.19550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.41700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.64750 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 27 CG OD1 ND2 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 -132.37 49.26 REMARK 500 ASP A 87 89.62 -156.26 REMARK 500 VAL A 103 -140.30 -124.37 REMARK 500 TYR A 105 113.93 -160.00 REMARK 500 ASN A 106 66.92 -155.12 REMARK 500 SER A 220 -128.09 -103.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 9ZQQ A 27 290 UNP A3FFV8 A3FFV8_ECOLX 31 291 SEQADV 9ZQQ ASN A 276 UNP A3FFV8 ARG 277 CONFLICT SEQRES 1 A 261 ASN SER VAL GLN GLN GLN LEU GLU ALA LEU GLU LYS SER SEQRES 2 A 261 SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASN THR ALA SEQRES 3 A 261 ASP ASN SER GLN ILE LEU TYR ARG ALA ASP GLU ARG PHE SEQRES 4 A 261 ALA MET CYS SER THR SER LYS VAL MET ALA ALA ALA ALA SEQRES 5 A 261 VAL LEU LYS GLN SER GLU SER ASP LYS HIS LEU LEU ASN SEQRES 6 A 261 GLN ARG VAL GLU ILE LYS LYS SER 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 GLY ALA ALA ALA LEU GLN TYR SER ASP SEQRES 9 A 261 ASN THR ALA MET ASN LYS LEU ILE ALA HIS LEU GLY GLY SEQRES 10 A 261 PRO ASP LYS VAL THR ALA PHE ALA ARG SER LEU 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 LEU ALA MET ALA GLN THR LEU LYS ASN LEU THR LEU GLY SEQRES 14 A 261 LYS ALA LEU ALA GLU THR GLN ARG ALA GLN LEU VAL THR SEQRES 15 A 261 TRP LEU LYS GLY ASN THR THR GLY SER ALA SER ILE ARG SEQRES 16 A 261 ALA GLY LEU PRO LYS SER TRP VAL 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 GLU ASN HIS ALA PRO LEU VAL LEU VAL THR SEQRES 19 A 261 TYR PHE THR GLN PRO GLU GLN LYS ALA GLU ASN ARG ASN SEQRES 20 A 261 ASP ILE LEU ALA ALA ALA ALA LYS ILE VAL THR HIS GLY SEQRES 21 A 261 PHE HET NXL A 301 17 HET FYG A 302 17 HETNAM NXL (2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2- HETNAM 2 NXL CARBOXAMIDE HETNAM FYG (2S,5R)-7-OXO-6-(SULFOOXY)-1,6- HETNAM 2 FYG DIAZABICYCLO[3.2.1]OCTANE-2-CARBOXAMIDE HETSYN NXL AVIBACTAM, BOUND FORM; NXL104, BOUND FORM HETSYN FYG AVIBACTAM FORMUL 2 NXL C7 H13 N3 O6 S FORMUL 3 FYG C7 H11 N3 O6 S FORMUL 4 HOH *214(H2 O) HELIX 1 AA1 SER A 28 SER A 39 1 12 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 VAL A 113 5 6 HELIX 7 AA7 LEU A 119 TYR A 129 1 11 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 LEU A 195 1 14 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 THR A 287 1 13 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 TYR A 264 N GLY A 45 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 VAL A 230 O TRP A 251 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 GLY A 115 N ILE A 97 LINK OG SER A 70 CAN NXL A 301 1555 1555 1.37 CISPEP 1 GLU A 166 PRO A 167 0 4.94 CRYST1 44.834 73.295 78.391 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 0.022305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012757 0.00000 CONECT 323 1972 CONECT 1971 1972 CONECT 1972 323 1971 1973 CONECT 1973 1972 1974 1975 CONECT 1974 1973 1981 CONECT 1975 1973 1976 1979 CONECT 1976 1975 1977 1978 CONECT 1977 1976 CONECT 1978 1976 CONECT 1979 1975 1980 CONECT 1980 1979 1981 CONECT 1981 1974 1980 1982 CONECT 1982 1981 1983 CONECT 1983 1982 1984 CONECT 1984 1983 1985 1986 1987 CONECT 1985 1984 CONECT 1986 1984 CONECT 1987 1984 CONECT 1988 1991 1997 2003 CONECT 1989 1990 1993 CONECT 1990 1989 1991 CONECT 1991 1988 1990 1995 CONECT 1992 1993 1995 CONECT 1993 1989 1992 1996 CONECT 1994 1995 1996 1998 CONECT 1995 1991 1992 1994 CONECT 1996 1993 1994 1999 CONECT 1997 1988 CONECT 1998 1994 CONECT 1999 1996 2004 CONECT 2000 2004 CONECT 2001 2004 CONECT 2002 2004 CONECT 2003 1988 CONECT 2004 1999 2000 2001 2002 MASTER 224 0 2 14 9 0 0 6 2217 1 35 21 END