HEADER HYDROLASE 15-NOV-18 6N3K TITLE CRYSTAL STRUCTURE OF AN EPOXIDE HYDROLASE FROM TRICHODERMA REESEI IN TITLE 2 COMPLEX WITH INHIBITOR 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPOXIDE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA REESEI QM9414; SOURCE 3 ORGANISM_TAXID: 334564; SOURCE 4 GENE: TREH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS TRICHODERMA REESEI, EPOXIDE HYDROLASE, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.S.DE OLIVEIRA,P.P.ADRIANI,J.A.RIBEIRO,C.MORISSEAU,B.D.HAMMOCK, AUTHOR 2 M.V.DIAS,F.S.CHAMBERGO REVDAT 3 11-OCT-23 6N3K 1 REMARK REVDAT 2 18-DEC-19 6N3K 1 REMARK REVDAT 1 20-NOV-19 6N3K 0 JRNL AUTH G.S.DE OLIVEIRA,P.P.ADRIANI,J.A.RIBEIRO,C.MORISSEAU, JRNL AUTH 2 B.D.HAMMOCK,M.V.B.DIAS,F.S.CHAMBERGO JRNL TITL THE MOLECULAR STRUCTURE OF AN EPOXIDE HYDROLASE FROM JRNL TITL 2 TRICHODERMA REESEI IN COMPLEX WITH UREA OR AMIDE-BASED JRNL TITL 3 INHIBITORS. JRNL REF INT. J. BIOL. MACROMOL. V. 129 653 2019 JRNL REFN ISSN 1879-0003 JRNL PMID 30771398 JRNL DOI 10.1016/J.IJBIOMAC.2019.02.070 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17685 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 868 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 37.9465 - 3.9964 0.98 2904 161 0.1812 0.2430 REMARK 3 2 3.9964 - 3.1725 0.99 2825 124 0.1656 0.2179 REMARK 3 3 3.1725 - 2.7716 1.00 2815 126 0.1830 0.2649 REMARK 3 4 2.7716 - 2.5183 1.00 2752 176 0.1913 0.2579 REMARK 3 5 2.5183 - 2.3378 1.00 2761 148 0.1960 0.2981 REMARK 3 6 2.3378 - 2.2000 1.00 2760 133 0.1913 0.2479 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.67 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 2740 REMARK 3 ANGLE : 0.882 3718 REMARK 3 CHIRALITY : 0.048 387 REMARK 3 PLANARITY : 0.006 487 REMARK 3 DIHEDRAL : 16.599 1623 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 6N3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.52 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.48 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17796 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.19000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 1.04000 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 2.6.0 REMARK 200 STARTING MODEL: 5URO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM 3-MORPHOLINOPROPANE-1-SULFONIC REMARK 280 ACID (MOPS) PH 6.5, 40 MM POTASSIUM BROMIDE AND 44.6% PEG 4000, REMARK 280 PH 6.52, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.63800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.55150 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.63800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.55150 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 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 GLU A 227 CG CD OE1 OE2 REMARK 470 LYS A 295 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 82 CZ ARG A 82 NH2 -0.085 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 ASP A 48 -164.03 -117.39 REMARK 500 ALA A 76 -127.12 54.75 REMARK 500 ASP A 116 -129.48 62.09 REMARK 500 CYS A 140 -46.83 72.15 REMARK 500 ASP A 303 64.37 -153.24 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 K9V A 401 DBREF 6N3K A 1 336 PDB 6N3K 6N3K 1 336 SEQRES 1 A 336 MET ASP THR SER LYS LEU LYS PRO ASN ASP PRO ARG VAL SEQRES 2 A 336 LYS TYR GLU THR LYS GLN ILE ARG GLY LYS THR TYR SER SEQRES 3 A 336 TYR ILE LEU GLY GLU PRO ALA GLY PRO LYS LEU GLU THR SEQRES 4 A 336 VAL VAL LEU VAL HIS GLY TRP PRO ASP MET ALA PHE GLY SEQRES 5 A 336 TRP ARG HIS GLN ILE PRO TYR LEU MET SER LEU GLY PHE SEQRES 6 A 336 GLN VAL VAL ALA PRO ASN MET LEU GLY TYR ALA GLY THR SEQRES 7 A 336 ASP ALA PRO ARG ASP LEU SER GLN PHE THR LEU LYS SER SEQRES 8 A 336 VAL SER ALA ASP ILE ALA GLU LEU ALA ARG SER PHE VAL SEQRES 9 A 336 GLY GLN ASP GLY GLN ILE VAL LEU GLY GLY HIS ASP TRP SEQRES 10 A 336 GLY GLY ALA VAL VAL TRP ARG THR ALA TYR TYR HIS PRO SEQRES 11 A 336 GLU LEU VAL LYS ALA VAL PHE SER VAL CYS THR PRO LEU SEQRES 12 A 336 HIS PRO LEU SER ALA GLU TYR LYS PRO LEU GLU ASP ILE SEQRES 13 A 336 VAL ALA ALA GLY HIS MET LEU ASN PHE LYS TYR GLN LEU SEQRES 14 A 336 GLN LEU LYS GLY PRO ASP VAL GLU ALA ARG ILE GLN GLY SEQRES 15 A 336 LYS ASP MET LEU ARG ARG PHE PHE ARG ALA MET PHE GLY SEQRES 16 A 336 GLY ARG GLY PRO ASN GLY GLU ALA GLY PHE SER THR SER SEQRES 17 A 336 ASP GLY VAL HIS PHE ASP VAL LEU ASP LYS ILE GLY ALA SEQRES 18 A 336 PRO PRO LEU LEU ASP GLU GLN GLU LEU GLU TYR TYR VAL SEQRES 19 A 336 GLU GLN TYR ALA LEU GLN GLU ALA PRO GLU LEU ARG GLY SEQRES 20 A 336 PRO LEU ASN TRP TYR ARG THR ARG GLU LEU ASN ALA LYS SEQRES 21 A 336 ASP GLU MET ASP ARG ALA LYS ASN GLY PRO PRO LEU ARG SEQRES 22 A 336 PHE GLU MET PRO ALA LEU PHE VAL ALA ALA SER LYS ASP SEQRES 23 A 336 ASN ALA LEU PRO PRO ALA MET SER LYS GLY MET ASP ALA SEQRES 24 A 336 PHE TYR LYS ASP LEU THR ARG ALA GLU VAL ASP ALA THR SEQRES 25 A 336 HIS TRP ALA LEU THR GLN ALA GLY ASP GLU VAL ASN ARG SEQRES 26 A 336 VAL ILE GLY GLU TRP LEU ASN LYS ALA LEU GLY HET K9V A 401 29 HETNAM K9V N-{CIS-4-[(2,6-DIFLUOROPHENYL)METHOXY]CYCLOHEXYL}-N'- HETNAM 2 K9V (3-PHENYLPROPYL)UREA FORMUL 2 K9V C23 H28 F2 N2 O2 FORMUL 3 HOH *152(H2 O) HELIX 1 AA1 MET A 49 ARG A 54 5 6 HELIX 2 AA2 HIS A 55 LEU A 63 1 9 HELIX 3 AA3 ASP A 83 PHE A 87 5 5 HELIX 4 AA4 THR A 88 GLY A 105 1 18 HELIX 5 AA5 ASP A 116 HIS A 129 1 14 HELIX 6 AA6 PRO A 152 ALA A 159 1 8 HELIX 7 AA7 MET A 162 PHE A 165 5 4 HELIX 8 AA8 LYS A 166 GLY A 173 1 8 HELIX 9 AA9 PRO A 174 ILE A 180 1 7 HELIX 10 AB1 GLN A 181 PHE A 194 1 14 HELIX 11 AB2 PHE A 213 ILE A 219 5 7 HELIX 12 AB3 ASP A 226 ALA A 238 1 13 HELIX 13 AB4 LEU A 245 ASN A 250 1 6 HELIX 14 AB5 TRP A 251 ARG A 253 5 3 HELIX 15 AB6 THR A 254 ASN A 268 1 15 HELIX 16 AB7 PRO A 290 LYS A 295 5 6 HELIX 17 AB8 GLY A 296 TYR A 301 5 6 HELIX 18 AB9 TRP A 314 ALA A 319 1 6 HELIX 19 AC1 ALA A 319 LEU A 335 1 17 SHEET 1 AA1 8 LYS A 14 ILE A 20 0 SHEET 2 AA1 8 LYS A 23 GLY A 30 -1 O LYS A 23 N ILE A 20 SHEET 3 AA1 8 GLN A 66 PRO A 70 -1 O VAL A 67 N GLY A 30 SHEET 4 AA1 8 THR A 39 VAL A 43 1 N VAL A 40 O GLN A 66 SHEET 5 AA1 8 ILE A 110 HIS A 115 1 O GLY A 113 N VAL A 41 SHEET 6 AA1 8 VAL A 133 VAL A 139 1 O VAL A 139 N GLY A 114 SHEET 7 AA1 8 ALA A 278 LYS A 285 1 O VAL A 281 N SER A 138 SHEET 8 AA1 8 LEU A 304 THR A 312 1 O THR A 305 N ALA A 278 SHEET 1 AA2 2 PHE A 205 SER A 206 0 SHEET 2 AA2 2 GLY A 210 VAL A 211 -1 O GLY A 210 N SER A 206 CISPEP 1 TRP A 46 PRO A 47 0 -9.29 CISPEP 2 ALA A 242 PRO A 243 0 -8.65 SITE 1 AC1 13 TRP A 46 ASP A 116 TRP A 117 THR A 141 SITE 2 AC1 13 PRO A 142 HIS A 144 PHE A 165 TYR A 167 SITE 3 AC1 13 GLN A 168 MET A 193 TYR A 252 TRP A 314 SITE 4 AC1 13 HOH A 625 CRYST1 50.073 77.276 87.103 90.00 90.00 90.00 P 2 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 0.019971 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011481 0.00000