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- PDB-6f4k: Crystal structure of glutathione transferase Omega 3S from Tramet... -

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Basic information

Entry
Database: PDB / ID: 6f4k
TitleCrystal structure of glutathione transferase Omega 3S from Trametes versicolor in complex with hexyl-glutathione
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-HEXYLGLUTATHIONE / DI(HYDROXYETHYL)ETHER / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
DepositionNov 29, 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)56,65310
Polymers55,0532
Non-polymers1,6008
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-36 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.530, 104.140, 107.590
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 (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E145*PLUS

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Non-polymers , 5 types, 528 molecules

#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H30N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


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


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
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: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→47.8 Å / Num. obs: 82389 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.2
Reflection shellResolution: 1.55→1.59 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: 1.55→47.795 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 4114 5 %
Rwork0.1613 --
obs0.1624 82340 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→47.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 104 520 4420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114019
X-RAY DIFFRACTIONf_angle_d1.2295457
X-RAY DIFFRACTIONf_dihedral_angle_d17.4322405
X-RAY DIFFRACTIONf_chiral_restr0.061579
X-RAY DIFFRACTIONf_plane_restr0.01716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56830.28431290.26542453X-RAY DIFFRACTION91
1.5683-1.58740.27511350.25762564X-RAY DIFFRACTION94
1.5874-1.60750.26391380.23972612X-RAY DIFFRACTION98
1.6075-1.62860.28591420.2252700X-RAY DIFFRACTION99
1.6286-1.6510.29461390.22132643X-RAY DIFFRACTION100
1.651-1.67450.2531410.2232683X-RAY DIFFRACTION99
1.6745-1.69950.271410.20312679X-RAY DIFFRACTION100
1.6995-1.72610.22521400.19372666X-RAY DIFFRACTION100
1.7261-1.75440.23191430.17942711X-RAY DIFFRACTION100
1.7544-1.78460.20531410.17952674X-RAY DIFFRACTION100
1.7846-1.81710.1881420.182691X-RAY DIFFRACTION100
1.8171-1.85210.20411410.17332687X-RAY DIFFRACTION100
1.8521-1.88990.20271430.16852709X-RAY DIFFRACTION100
1.8899-1.9310.2031420.16472705X-RAY DIFFRACTION100
1.931-1.97590.17531410.1652687X-RAY DIFFRACTION100
1.9759-2.02530.18641450.15862740X-RAY DIFFRACTION100
2.0253-2.080.17511410.15252683X-RAY DIFFRACTION100
2.08-2.14120.17571420.15292700X-RAY DIFFRACTION100
2.1412-2.21040.1561430.13812715X-RAY DIFFRACTION100
2.2104-2.28940.15351430.14312711X-RAY DIFFRACTION100
2.2894-2.3810.16431420.13982723X-RAY DIFFRACTION100
2.381-2.48940.17451420.14442706X-RAY DIFFRACTION100
2.4894-2.62060.17491450.14972746X-RAY DIFFRACTION100
2.6206-2.78480.15581430.14642721X-RAY DIFFRACTION100
2.7848-2.99980.19161440.15432739X-RAY DIFFRACTION99
2.9998-3.30160.18081450.15662755X-RAY DIFFRACTION100
3.3016-3.77920.16371440.15252750X-RAY DIFFRACTION99
3.7792-4.76070.14681480.13642798X-RAY DIFFRACTION99
4.7607-47.81760.19191490.17352875X-RAY DIFFRACTION97

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