HEADER HYDROLASE 22-JAN-18 6C78 TITLE SUBSTRATE BINDING INDUCES CONFORMATIONAL CHANGES IN A CLASS A BETA TITLE 2 LACTAMASE THAT PRIMES IT FOR CATALYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE TOHO-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 32-291; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES 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 HYDROLASE EXPDTA NEUTRON DIFFRACTION AUTHOR P.S.LANGAN,V.G.VANDAVASI,S.J.COOPER,K.L.WEISS,S.L.GINELL,J.M.PARKS, AUTHOR 2 L.COATES REVDAT 2 13-MAR-24 6C78 1 REMARK REVDAT 1 21-MAR-18 6C78 0 JRNL AUTH P.S.LANGAN,V.G.VANDAVASI,S.J.COOPER,K.L.WEISS,S.L.GINELL, JRNL AUTH 2 J.M.PARKS,L.COATES JRNL TITL SUBSTRATE BINDING INDUCES CONFORMATIONAL CHANGES IN A CLASS JRNL TITL 2 A BETA-LACTAMASE THAT PRIME IT FOR CATALYSIS JRNL REF ACS CATALYSIS V. 8 2428 2018 JRNL REFN ESSN 2155-5435 JRNL DOI 10.1021/ACSCATAL.7B04114 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 3 NUMBER OF REFLECTIONS : 27135 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6C78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000232097. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 03-JAN-16 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 6.10 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : SPALLATION SOURCE REMARK 230 BEAMLINE : MANDI REMARK 230 WAVELENGTH OR RANGE (A) : 2-4 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : CMOS REMARK 230 DETECTOR MANUFACTURER : HAMAMATSU C10158DK REMARK 230 INTENSITY-INTEGRATION SOFTWARE : MANTID REMARK 230 DATA SCALING SOFTWARE : LAUEVIEW REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 27135 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 230 RESOLUTION RANGE LOW (A) : 14.760 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 230 DATA REDUNDANCY : 4.890 REMARK 230 R MERGE (I) : 0.15300 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 12.2000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 230 COMPLETENESS FOR SHELL (%) : 65.4 REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : 0.22900 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 3.300 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 230 SOFTWARE USED : NULL REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL 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 PREPARED IN D2O, PH 6.1, BATCH MODE, TEMPERATURE 293K, REMARK 280 PH 6.10 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 66.26000 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 33.13000 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 33.13000 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 66.26000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 24.0 KCAL/MOL 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 ALA A 27 REMARK 465 PHE A 290 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 DOD A 346 D1 DOD A 398 1.29 REMARK 500 DD21 ASN A 274 O DOD A 319 1.49 REMARK 500 O LEU A 81 DG SER A 84 1.56 REMARK 500 OD2 ASP A 176 D2 DOD A 323 1.57 REMARK 500 O DOD A 346 O DOD A 398 1.99 REMARK 500 OE2 GLU A 158 O DOD A 301 2.03 REMARK 500 O SER A 218 O DOD A 302 2.09 REMARK 500 O ALA A 272 O DOD A 303 2.19 REMARK 500 OE1 GLU A 201 O DOD A 304 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 -144.60 50.53 REMARK 500 ALA A 70 1.49 -68.91 REMARK 500 VAL A 103 -134.56 -114.22 REMARK 500 TYR A 105 101.56 33.74 REMARK 500 SER A 220 -128.72 -102.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 6C78 A 28 290 UNP Q47066 BLT1_ECOLX 32 291 SEQADV 6C78 ALA A 27 UNP Q47066 EXPRESSION TAG SEQADV 6C78 ALA A 70 UNP Q47066 SER 73 CONFLICT SEQADV 6C78 ASN A 274 UNP Q47066 ARG 275 CONFLICT SEQADV 6C78 ASN A 276 UNP Q47066 ARG 277 CONFLICT SEQRES 1 A 261 ALA 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 ALA 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 FORMUL 2 DOD *101(D2 O) HELIX 1 AA1 SER A 28 GLY A 41 1 14 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 LYS A 98 LEU A 102 5 5 HELIX 5 AA5 ILE A 108 VAL A 113 5 6 HELIX 6 AA6 LEU A 119 TYR A 129 1 11 HELIX 7 AA7 ASP A 131 GLY A 143 1 13 HELIX 8 AA8 GLY A 144 LEU A 155 1 12 HELIX 9 AA9 PRO A 167 THR A 171 5 5 HELIX 10 AB1 THR A 182 GLY A 196 1 15 HELIX 11 AB2 ALA A 200 GLY A 213 1 14 HELIX 12 AB3 SER A 220 LEU A 225 5 6 HELIX 13 AB4 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 GLY A 232 O VAL A 249 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 GLU A 96 0 SHEET 2 AA3 2 THR A 116 THR A 118 -1 O MET A 117 N VAL A 95 CISPEP 1 GLU A 166 PRO A 167 0 6.73 CRYST1 73.400 73.400 99.390 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 0.013624 0.007866 0.000000 0.00000 SCALE2 0.000000 0.015732 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010061 0.00000