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- PDB-6f6a: Crystal structure of glutathione transferase Omega 3S from Tramet... -

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Basic information

Entry
Database: PDB / ID: 6f6a
TitleCrystal structure of glutathione transferase Omega 3S from Trametes versicolor in complex with dihydrowogonin from wild-cherry extract
Componentsglutathione transferase
KeywordsTRANSFERASE / Glutathione / fungi / polyphenols / wood decayers
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / metal ion binding / cytoplasm
Similarity search - Function
: / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
S-Dihydrowogonin / GLUTATHIONE / DI(HYDROXYETHYL)ETHER / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchwartz, M. / Favier, F. / Didierjean, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LABX-0002-01 France
CNRS-University of LorrainePEPS MIRABELLE 2016 France
CitationJournal: Sci Rep / Year: 2018
Title: Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor.
Authors: Schwartz, M. / Perrot, T. / Aubert, E. / Dumarcay, S. / Favier, F. / Gerardin, P. / Morel-Rouhier, M. / Mulliert, G. / Saiag, F. / Didierjean, C. / Gelhaye, E.
History
DepositionDec 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glutathione transferase
B: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,76511
Polymers55,0532
Non-polymers1,7129
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-17 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.520, 104.490, 107.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein glutathione transferase


Mass: 27526.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor (turkey-tail fungus)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E145*PLUS

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Non-polymers , 7 types, 316 molecules

#2: Chemical ChemComp-CU5 / S-Dihydrowogonin


Mass: 286.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 278 K / Method: microbatch
Details: 30 % PEG 400 0.2 M calcium acetate 0.1 M acetate buffer, pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→47.97 Å / Num. obs: 63676 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.8
Reflection shellResolution: 1.7→1.74 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F43

6f43


Resolution: 1.7→45.483 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 3183 5 %
Rwork0.1622 --
obs0.1637 63665 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 115 307 4218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134035
X-RAY DIFFRACTIONf_angle_d1.2725487
X-RAY DIFFRACTIONf_dihedral_angle_d16.9332397
X-RAY DIFFRACTIONf_chiral_restr0.064579
X-RAY DIFFRACTIONf_plane_restr0.01718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72540.25161370.22642605X-RAY DIFFRACTION100
1.7254-1.75240.22031370.21252609X-RAY DIFFRACTION100
1.7524-1.78110.24461360.20742585X-RAY DIFFRACTION100
1.7811-1.81180.24251370.19872594X-RAY DIFFRACTION100
1.8118-1.84470.21671360.1872580X-RAY DIFFRACTION100
1.8447-1.88020.21971370.18272610X-RAY DIFFRACTION100
1.8802-1.91860.21481350.17312570X-RAY DIFFRACTION100
1.9186-1.96030.18341390.16962637X-RAY DIFFRACTION100
1.9603-2.00590.22941360.16752582X-RAY DIFFRACTION100
2.0059-2.05610.20381370.16462606X-RAY DIFFRACTION100
2.0561-2.11170.19081390.16682638X-RAY DIFFRACTION100
2.1117-2.17380.20351360.15492589X-RAY DIFFRACTION100
2.1738-2.2440.18681380.14892624X-RAY DIFFRACTION100
2.244-2.32420.18161370.15112603X-RAY DIFFRACTION100
2.3242-2.41720.19851390.14832631X-RAY DIFFRACTION100
2.4172-2.52720.20221380.15342629X-RAY DIFFRACTION100
2.5272-2.66050.20591380.15852618X-RAY DIFFRACTION100
2.6605-2.82710.20191400.15332658X-RAY DIFFRACTION100
2.8271-3.04540.19321380.16332630X-RAY DIFFRACTION100
3.0454-3.35170.21331410.172666X-RAY DIFFRACTION100
3.3517-3.83650.16071400.15852676X-RAY DIFFRACTION100
3.8365-4.83280.1581430.14042712X-RAY DIFFRACTION100
4.8328-45.49910.1841490.16892830X-RAY DIFFRACTION99

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