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HEADER HYDROLASE 11-FEB-17 5URO
TITLE STRUCTURE OF A SOLUBLE EPOXIDE HYDROLASE IDENTIFIED IN TRICHODERMA
TITLE 2 REESEI
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PREDICTED PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HYPOCREA JECORINA (STRAIN QM6A);
SOURCE 3 ORGANISM_TAXID: 431241;
SOURCE 4 STRAIN: QM6A;
SOURCE 5 GENE: TRIREDRAFT_53220;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 55989;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 585055
KEYWDS EPOXIDE HYDROLASE; TRICHODERMA REESEI, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.WILSON,G.DE OLIVEIRA,F.CHAMBERGO,M.V.B.DIAS
REVDAT 1 31-MAY-17 5URO 0
JRNL AUTH C.WILSON,G.S.DE OLIVEIRA,P.P.ADRIANI,F.S.CHAMBERGO,
JRNL AUTH 2 M.V.B.DIAS
JRNL TITL STRUCTURE OF A SOLUBLE EPOXIDE HYDROLASE IDENTIFIED IN
JRNL TITL 2 TRICHODERMA REESEI.
JRNL REF BIOCHIM. BIOPHYS. ACTA 2017
JRNL REFN ISSN 0006-3002
JRNL PMID 28502798
JRNL DOI 10.1016/J.BBAPAP.2017.05.004
REMARK 2
REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.8.4_1496
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) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.32
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 74551
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) : 0.183
REMARK 3 FREE R VALUE : 0.211
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050
REMARK 3 FREE R VALUE TEST SET COUNT : 3768
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 : 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) : 25.620
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.00
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 5URO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-17.
REMARK 100 THE DEPOSITION ID IS D_1000226389.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-AUG-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY
REMARK 200 BEAMLINE : P13 (MX1)
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.976250
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : AREA DETECTOR
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74551
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.701
REMARK 200 RESOLUTION RANGE LOW (A) : 44.320
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0
REMARK 200 DATA REDUNDANCY : 12.90
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 1.3400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
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 2.5.6, PHASER
REMARK 200 STARTING MODEL: 3ANS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.50
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, VAPOR DIFFUSION, TEMPERATURE
REMARK 280 298K
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 39.14050
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.68600
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.14050
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.68600
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 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: 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 OAG 8LD A 401 O HOH A 501 1.92
REMARK 500 O HOH A 586 O HOH A 655 2.14
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 PRO A 47 79.27 -100.39
REMARK 500 ASP A 48 -160.88 -114.11
REMARK 500 ALA A 76 -124.94 49.64
REMARK 500 ASP A 116 -133.31 59.52
REMARK 500 CYS A 140 -38.46 77.90
REMARK 500 LYS A 285 32.22 -97.62
REMARK 500 LYS A 295 -88.52 -23.35
REMARK 500 ASP A 303 70.55 -151.94
REMARK 500 THR A 312 -165.31 -74.97
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 8LD A 401
DBREF 5URO A 1 335 UNP G0R7E2 G0R7E2_HYPJQ 1 335
SEQADV 5URO ALA A 33 UNP G0R7E2 GLN 33 CONFLICT
SEQADV 5URO GLY A 336 UNP G0R7E2 EXPRESSION TAG
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 8LD A 401 7
HETNAM 8LD 2,2'-OXYDI(ETHYN-1-OL)
FORMUL 2 8LD C4 H2 O3
FORMUL 3 HOH *179(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 TRP A 251 1 7
HELIX 14 AB5 THR A 254 ASN A 268 1 15
HELIX 15 AB6 PRO A 290 LYS A 295 5 6
HELIX 16 AB7 GLY A 296 TYR A 301 5 6
HELIX 17 AB8 TRP A 314 ALA A 319 1 6
HELIX 18 AB9 ALA A 319 GLY A 336 1 18
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 PHE A 137 N LEU A 112
SHEET 7 AA1 8 ALA A 278 ALA A 283 1 O VAL A 281 N SER A 138
SHEET 8 AA1 8 LEU A 304 VAL A 309 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 -9.03
CISPEP 2 ALA A 242 PRO A 243 0 -4.00
SITE 1 AC1 9 TYR A 15 GLU A 16 SER A 26 ILE A 28
SITE 2 AC1 9 ASN A 71 TYR A 232 GLN A 236 HOH A 501
SITE 3 AC1 9 HOH A 570
CRYST1 51.427 78.281 87.372 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 0.019445 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012774 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011445 0.00000
TER 2646 GLY A 336
MASTER 236 0 1 18 10 0 3 6 2823 1 7 26
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