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- PDB-6f68: Crystal structure glutathione transferase Omega 3S from Trametes ... -

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Basic information

Entry
Database: PDB / ID: 6f68
TitleCrystal structure glutathione transferase Omega 3S from Trametes versicolor in complex with 2,4,4'-trihydroxybenzophenone
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
(2,4-dihydroxyphenyl)(4-hydroxyphenyl)methanone / GLUTATHIONE / DI(HYDROXYETHYL)ETHER / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 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)56,65311
Polymers55,0532
Non-polymers1,6009
Water6,287349
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-19 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.680, 104.790, 108.290
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, 358 molecules

#2: Chemical ChemComp-4EU / (2,4-dihydroxyphenyl)(4-hydroxyphenyl)methanone


Mass: 230.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10O4 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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.: 349 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
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: 1.696→47.2 Å / Num. obs: 64275 / % possible obs: 99.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.413 / Num. unique obs: 4473

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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: 1.696→47.164 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 3214 5 %
Rwork0.1613 --
obs0.1628 64266 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.696→47.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 107 349 4252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124036
X-RAY DIFFRACTIONf_angle_d1.2215488
X-RAY DIFFRACTIONf_dihedral_angle_d16.8522402
X-RAY DIFFRACTIONf_chiral_restr0.06578
X-RAY DIFFRACTIONf_plane_restr0.01720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6962-1.72150.25651250.20032376X-RAY DIFFRACTION91
1.7215-1.74840.2111400.18772668X-RAY DIFFRACTION100
1.7484-1.77710.24531380.18532615X-RAY DIFFRACTION100
1.7771-1.80770.21571400.18042654X-RAY DIFFRACTION100
1.8077-1.84060.23011370.17872619X-RAY DIFFRACTION100
1.8406-1.8760.20191410.1782662X-RAY DIFFRACTION100
1.876-1.91430.23461360.17872597X-RAY DIFFRACTION100
1.9143-1.95590.18711400.16652664X-RAY DIFFRACTION100
1.9559-2.00140.20291390.16222627X-RAY DIFFRACTION100
2.0014-2.05140.2131400.16532664X-RAY DIFFRACTION100
2.0514-2.10690.21851390.16732649X-RAY DIFFRACTION100
2.1069-2.16890.21471380.15982617X-RAY DIFFRACTION100
2.1689-2.23890.20911410.15072676X-RAY DIFFRACTION100
2.2389-2.31890.18381400.15182668X-RAY DIFFRACTION100
2.3189-2.41180.17561400.15062643X-RAY DIFFRACTION100
2.4118-2.52150.19651400.15432677X-RAY DIFFRACTION100
2.5215-2.65450.18511400.16042661X-RAY DIFFRACTION100
2.6545-2.82080.21911410.15822661X-RAY DIFFRACTION100
2.8208-3.03850.17561400.17072665X-RAY DIFFRACTION99
3.0385-3.34420.19111420.17412694X-RAY DIFFRACTION99
3.3442-3.82790.1811420.15742707X-RAY DIFFRACTION100
3.8279-4.82210.1481440.13722733X-RAY DIFFRACTION99
4.8221-47.18260.18871510.16562855X-RAY DIFFRACTION99

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