HEADER HYDROLASE 08-JUL-16 5KSC TITLE E166A/R274N/R276N TOHO-1 BETA-LACTAMASE AZTREONAM ACYL-ENZYME TITLE 2 INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE TOHO-1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: AZTREONAM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-LACTAMASE, AZTREONAM, ACYL-INTERMEDIATE, HYDROLASE EXPDTA NEUTRON DIFFRACTION AUTHOR V.G.VANDAVASI,P.S.LANGAN,K.WEISS,J.M.PARKS,J.B.COOPER,S.L.GINELL, AUTHOR 2 L.COATES REVDAT 5 04-DEC-19 5KSC 1 REMARK REVDAT 4 06-JUN-18 5KSC 1 REMARK REVDAT 3 20-SEP-17 5KSC 1 REMARK REVDAT 2 11-JAN-17 5KSC 1 JRNL REVDAT 1 09-NOV-16 5KSC 0 JRNL AUTH V.G.VANDAVASI,P.S.LANGAN,K.L.WEISS,J.M.PARKS,J.B.COOPER, JRNL AUTH 2 S.L.GINELL,L.COATES JRNL TITL ACTIVE-SITE PROTONATION STATES IN AN ACYL-ENZYME JRNL TITL 2 INTERMEDIATE OF A CLASS A BETA-LACTAMASE WITH A MONOBACTAM JRNL TITL 3 SUBSTRATE. JRNL REF ANTIMICROB. AGENTS V. 61 2017 JRNL REF 2 CHEMOTHER. JRNL REFN ESSN 1098-6596 JRNL PMID 27795378 JRNL DOI 10.1128/AAC.01636-16 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.1 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1966 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2011.8 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2024.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5KSC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222670. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 03-MAR-15 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 6.10 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : NULL REMARK 230 WAVELENGTH OR RANGE (A) : 2-4 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : AREA DETECTOR REMARK 230 DETECTOR MANUFACTURER : ORNL ANGER CAMERA REMARK 230 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 230 DATA SCALING SOFTWARE : NULL REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 13173 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 230 RESOLUTION RANGE LOW (A) : 14.730 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 71.5 REMARK 230 DATA REDUNDANCY : 3.100 REMARK 230 R MERGE (I) : 0.16000 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 10.1000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 230 COMPLETENESS FOR SHELL (%) : 50.1 REMARK 230 DATA REDUNDANCY IN SHELL : 2.00 REMARK 230 R MERGE FOR SHELL (I) : 0.26000 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 4.200 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : SHELX REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 300 MICROLITERS OF A 10 MG/ML PROTEIN REMARK 280 CONCENTRATION IN A SOLUTION CONTAINING 2.0 M AMMONIUM SULFATE REMARK 280 AND 0.1 M SODIUM CITRATE (PH 6.1) PREPARED IN D2O., BATCH MODE, REMARK 280 TEMPERATURE 293.15K 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 66.06200 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 33.03100 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 33.03100 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 66.06200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 ASP A 100 D2 DOD A 404 1.45 REMARK 500 O PRO A 173 D2 DOD A 410 1.57 REMARK 500 O GLY A 216 D2 DOD A 405 1.58 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 68 -130.05 57.22 REMARK 500 VAL A 102 -145.06 -124.49 REMARK 500 ASN A 105 75.89 -166.05 REMARK 500 SER A 219 -116.27 -85.50 REMARK 500 ASN A 252 29.62 -142.26 REMARK 500 LYS A 268 47.49 -90.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AZR A 301 DBREF 5KSC A 27 287 UNP Q47066 BLT1_ECOLX 31 291 SEQADV 5KSC ALA A 165 UNP Q47066 GLU 169 ENGINEERED MUTATION SEQADV 5KSC ASN A 271 UNP Q47066 ARG 275 ENGINEERED MUTATION SEQADV 5KSC ASN A 273 UNP Q47066 ARG 277 ENGINEERED MUTATION 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 ALA 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 AZR A 301 28 HETNAM AZR 2-({[(1Z)-1-(2-AMINO-1,3-THIAZOL-4-YL)-2-OXO-2-{[(2S, HETNAM 2 AZR 3S)-1-OXO-3-(SULFOAMINO)BUTAN-2- HETNAM 3 AZR YL]AMINO}ETHYLIDENE]AMINO}OXY)-2-METHYLPROPANOIC ACID HETSYN AZR AZTREONAM, OPEN FORM FORMUL 2 AZR C13 H19 N5 O8 S2 FORMUL 3 DOD *29(D2 O) HELIX 1 AA1 SER A 28 GLY A 41 1 14 HELIX 2 AA2 CYS A 68 THR A 70 5 3 HELIX 3 AA3 SER A 71 GLU A 84 1 14 HELIX 4 AA4 LYS A 97 LEU A 101 5 5 HELIX 5 AA5 ILE A 107 VAL A 112 5 6 HELIX 6 AA6 THR A 117 TYR A 128 1 12 HELIX 7 AA7 ASP A 130 GLY A 142 1 13 HELIX 8 AA8 GLY A 143 LEU A 154 1 12 HELIX 9 AA9 PRO A 166 THR A 170 5 5 HELIX 10 AB1 THR A 181 LEU A 194 1 14 HELIX 11 AB2 ALA A 199 GLY A 212 1 14 HELIX 12 AB3 ILE A 220 LEU A 224 5 5 HELIX 13 AB4 ARG A 272 THR A 284 1 13 SHEET 1 AA1 5 GLN A 56 TYR A 59 0 SHEET 2 AA1 5 ARG A 43 ASN A 50 -1 N VAL A 46 O TYR A 59 SHEET 3 AA1 5 LEU A 256 THR A 263 -1 O THR A 263 N ARG A 43 SHEET 4 AA1 5 THR A 242 TRP A 249 -1 N ILE A 248 O LEU A 256 SHEET 5 AA1 5 VAL A 229 SER A 236 -1 N GLY A 235 O ASN A 243 SHEET 1 AA2 2 PHE A 65 ALA A 66 0 SHEET 2 AA2 2 THR A 179 THR A 180 -1 O THR A 180 N PHE A 65 SHEET 1 AA3 2 GLU A 95 ILE A 96 0 SHEET 2 AA3 2 GLY A 114 THR A 115 -1 O GLY A 114 N ILE A 96 LINK OG SER A 69 C20 AZR A 301 1555 1555 1.35 CISPEP 1 ALA A 165 PRO A 166 0 -1.72 SITE 1 AC1 13 CYS A 68 SER A 69 ASN A 103 TYR A 104 SITE 2 AC1 13 SER A 129 ASN A 131 PRO A 166 ASN A 169 SITE 3 AC1 13 LYS A 233 THR A 234 GLY A 235 SER A 236 SITE 4 AC1 13 ASP A 238 CRYST1 73.296 73.296 99.093 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 0.013643 0.007877 0.000000 0.00000 SCALE2 0.000000 0.015754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010092 0.00000