HEADER LYASE 21-AUG-23 8KH3 TITLE CRYSTAL STRUCTURE OF KEMP ELIMINASE HG3.17 IN COMPLEXED WITH 5- TITLE 2 CYANOBENZOTRIAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: KEMP ELIMINASE HG3.17; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOASCUS AURANTIACUS; SOURCE 3 ORGANISM_TAXID: 5087; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KEMP ELIMINASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BUNZEL,T.MORI,D.HILVERT REVDAT 1 04-SEP-24 8KH3 0 JRNL AUTH A.BUNZEL,S.H.SCHNEIDER,J.A.KOZUCH,T.MORI,S.G.BOXER, JRNL AUTH 2 A.J.MULHOLLAND,D.HILVERT JRNL TITL EVOLUTION OF PREORGANIZED ELECTRIC FIELDS BOOSTS CATALYSIS JRNL TITL 2 IN A DESIGNER ENZYME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 18644 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1864 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 48.7200 - 4.7014 0.98 1392 156 0.1566 0.1868 REMARK 3 2 4.7014 - 3.7320 1.00 1333 147 0.1281 0.1572 REMARK 3 3 3.7320 - 3.2604 0.98 1293 144 0.1425 0.1712 REMARK 3 4 3.2604 - 2.9624 1.00 1305 145 0.1508 0.1688 REMARK 3 5 2.9624 - 2.7500 0.99 1287 142 0.1541 0.2139 REMARK 3 6 2.7500 - 2.5879 1.00 1287 144 0.1592 0.2214 REMARK 3 7 2.5879 - 2.4583 0.97 1255 139 0.1483 0.2192 REMARK 3 8 2.4583 - 2.3513 0.99 1278 143 0.1474 0.2091 REMARK 3 9 2.3513 - 2.2608 0.99 1271 141 0.1348 0.2194 REMARK 3 10 2.2608 - 2.1828 1.00 1274 140 0.1349 0.1745 REMARK 3 11 2.1828 - 2.1145 1.00 1290 143 0.1330 0.2103 REMARK 3 12 2.1145 - 2.0541 1.00 1252 139 0.1406 0.2009 REMARK 3 13 2.0541 - 2.0000 0.98 1263 141 0.1543 0.2129 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.820 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 : 0.008 2344 REMARK 3 ANGLE : 0.841 3197 REMARK 3 CHIRALITY : 0.049 358 REMARK 3 PLANARITY : 0.005 416 REMARK 3 DIHEDRAL : 3.175 1374 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 8KH3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300040237. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18690 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 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) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 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 (%): 36.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1M AMMONIUM SULFATE, 100MM SODIUM REMARK 280 ACETATE, PH 5.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 25.48400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.75800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.77650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.75800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.48400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.77650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 MET A -1 REMARK 465 ALA A 0 REMARK 465 GLU A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 GLN A 303 REMARK 465 GLY A 304 REMARK 465 SER A 305 REMARK 465 ILE A 306 REMARK 465 GLU A 307 REMARK 465 GLY A 308 REMARK 465 ARG A 309 REMARK 465 GLY A 310 REMARK 465 HIS A 311 REMARK 465 HIS A 312 REMARK 465 HIS A 313 REMARK 465 HIS A 314 REMARK 465 HIS A 315 REMARK 465 HIS A 316 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 VAL A 269 -65.11 -92.49 REMARK 500 THR A 280 65.62 33.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 8KH3 A -1 316 PDB 8KH3 8KH3 -1 316 SEQRES 1 A 318 MET ALA GLU ALA ALA GLN SER ILE ASP GLN LEU ILE LYS SEQRES 2 A 318 ALA ARG GLY LYS VAL TYR PHE GLY VAL ALA THR ASP GLN SEQRES 3 A 318 ASN ARG LEU THR THR GLY LYS ASN ALA ALA ILE ILE LYS SEQRES 4 A 318 ALA ASP PHE GLY MET VAL TRP PRO GLU ASN SER MET GLN SEQRES 5 A 318 TRP ASP ALA THR GLU PRO SER GLN GLY ASN PHE ASN PHE SEQRES 6 A 318 ALA GLY ALA ASP TYR LEU VAL ASN TRP ALA GLN GLN ASN SEQRES 7 A 318 GLY LYS LEU ILE GLY ALA GLY CYS LEU VAL TRP HIS ASN SEQRES 8 A 318 PHE LEU PRO SER TRP VAL SER SER ILE THR ASP LYS ASN SEQRES 9 A 318 THR LEU ILE ASN VAL MET LYS ASN HIS ILE THR THR LEU SEQRES 10 A 318 MET THR ARG TYR LYS GLY LYS ILE ARG THR TRP ASP VAL SEQRES 11 A 318 VAL GLY GLU ALA PHE ASN GLU ASP GLY SER LEU ARG GLN SEQRES 12 A 318 ASN VAL PHE LEU ASN VAL ILE GLY GLU ASP TYR ILE PRO SEQRES 13 A 318 ILE ALA PHE GLN THR ALA ARG ALA ALA ASP PRO ASN ALA SEQRES 14 A 318 LYS LEU TYR ILE MET ASP TYR ASN LEU ASP SER ALA SER SEQRES 15 A 318 TYR PRO LYS THR GLN ALA ILE VAL ASN ARG VAL LYS GLN SEQRES 16 A 318 TRP ARG ALA ALA GLY VAL PRO ILE ASP GLY ILE GLY SER SEQRES 17 A 318 GLN MET HIS LEU SER ALA GLY GLN GLY ALA GLY VAL LEU SEQRES 18 A 318 GLN ALA LEU PRO LEU LEU ALA SER ALA GLY THR PRO GLU SEQRES 19 A 318 VAL SER ILE LEU MET LEU ASP VAL ALA GLY ALA SER PRO SEQRES 20 A 318 THR ASP TYR VAL ASN VAL VAL ASN ALA CYS LEU ASN VAL SEQRES 21 A 318 GLN SER CYS VAL GLY ILE THR VAL MET GLY VAL ALA ASP SEQRES 22 A 318 PRO ASP SER ALA PHE ALA SER SER THR PRO LEU LEU PHE SEQRES 23 A 318 ASP GLY ASN PHE ASN PRO LYS PRO ALA TYR ASN ALA ILE SEQRES 24 A 318 VAL GLN ASP LEU GLN GLN GLY SER ILE GLU GLY ARG GLY SEQRES 25 A 318 HIS HIS HIS HIS HIS HIS HET VWF A 401 11 HET SO4 A 402 5 HETNAM VWF 1H-BENZOTRIAZOLE-5-CARBONITRILE HETNAM SO4 SULFATE ION HETSYN VWF 5-CYANOBENZOTRIAZOLE FORMUL 2 VWF C7 H4 N4 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *303(H2 O) HELIX 1 AA1 SER A 5 ARG A 13 1 9 HELIX 2 AA2 ASP A 23 THR A 28 1 6 HELIX 3 AA3 LYS A 31 PHE A 40 1 10 HELIX 4 AA4 GLN A 50 GLU A 55 1 6 HELIX 5 AA5 PHE A 63 ASN A 76 1 14 HELIX 6 AA6 PRO A 92 SER A 97 1 6 HELIX 7 AA7 ASP A 100 TYR A 119 1 20 HELIX 8 AA8 ASN A 142 ILE A 148 1 7 HELIX 9 AA9 ASP A 151 ASP A 164 1 14 HELIX 10 AB1 TYR A 181 ALA A 197 1 17 HELIX 11 AB2 GLN A 214 SER A 227 1 14 HELIX 12 AB3 SER A 244 VAL A 258 1 15 HELIX 13 AB4 ALA A 270 SER A 274 5 5 HELIX 14 AB5 PHE A 276 THR A 280 5 5 HELIX 15 AB6 LYS A 291 GLN A 302 1 12 SHEET 1 AA1 9 TYR A 17 THR A 22 0 SHEET 2 AA1 9 MET A 42 PRO A 45 1 O TRP A 44 N THR A 22 SHEET 3 AA1 9 LEU A 79 VAL A 86 1 O GLY A 81 N VAL A 43 SHEET 4 AA1 9 THR A 125 GLY A 130 1 O ASP A 127 N ALA A 82 SHEET 5 AA1 9 LYS A 168 TYR A 174 1 O LYS A 168 N TRP A 126 SHEET 6 AA1 9 GLY A 203 LEU A 210 1 O GLY A 205 N ILE A 171 SHEET 7 AA1 9 GLU A 232 VAL A 240 1 O LEU A 236 N SER A 206 SHEET 8 AA1 9 CYS A 261 VAL A 266 1 O THR A 265 N LEU A 238 SHEET 9 AA1 9 TYR A 17 THR A 22 1 N GLY A 19 O ILE A 264 SSBOND 1 CYS A 255 CYS A 261 1555 1555 2.07 CISPEP 1 GLY A 83 CYS A 84 0 3.35 CRYST1 50.968 57.553 91.516 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 0.019620 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010927 0.00000