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- PDB-6sr8: Crystal structure of glutathione transferase Omega 2C from Tramet... -

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Basic information

Entry
Database: PDB / ID: 6sr8
TitleCrystal structure of glutathione transferase Omega 2C from Trametes versicolor
ComponentsUncharacterized protein
KeywordsTRANSFERASE / glutathione transferase
Function / homology
Function and homology information


: / 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
GLUTATHIONE / GST N-terminal domain-containing protein
Similarity search - Component
Biological speciesTrametes versicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSchwartz, M. / Favier, F. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LAS-0002-01 France
CitationJournal: Fungal Genet Biol. / Year: 2021
Title: Diversity of Omega Glutathione Transferases in mushroom-forming fungi revealed by phylogenetic, transcriptomic, biochemical and structural approaches.
Authors: Perrot, T. / Schwartz, M. / Deroy, A. / Girardet, J.M. / Kohler, A. / Morel-Rouhier, M. / Favier, F. / Gelhaye, E. / Didierjean, C.
History
DepositionSep 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4714
Polymers54,8562
Non-polymers6152
Water6,954386
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4714
Polymers54,8562
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2830 Å2
ΔGint-24 kcal/mol
Surface area20800 Å2
MethodPISA
2
B: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4714
Polymers54,8562
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2910 Å2
ΔGint-22 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.490, 141.960, 65.370
Angle α, β, γ (deg.)90.000, 116.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

21A-584-

HOH

31B-431-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 27428.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor (strain FP-101664) (fungus)
Strain: FP-101664 / Gene: TRAVEDRAFT_67635 / Production host: Escherichia coli (E. coli) / References: UniProt: R7S7J5
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 20% (w/v) polyethylene glycol 4000, 10% (v/v) 2-Propanol and 0.1 M pH 7.5 HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979767 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979767 Å / Relative weight: 1
ReflectionResolution: 1.9→22.147 Å / Num. obs: 42824 / % possible obs: 97.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.064 / Net I/σ(I): 13.33
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.28 / Num. unique obs: 3095 / CC1/2: 0.96 / Rrim(I) all: 0.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HJS

6hjs


Resolution: 1.94→22.147 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.03
RfactorNum. reflection% reflection
Rfree0.2526 2010 5 %
Rwork0.1957 --
obs0.1985 40224 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.19 Å2 / Biso mean: 39.0508 Å2 / Biso min: 16.19 Å2
Refinement stepCycle: final / Resolution: 1.94→22.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 68 386 4097
Biso mean--30.41 36.34 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123788
X-RAY DIFFRACTIONf_angle_d1.0275145
X-RAY DIFFRACTIONf_chiral_restr0.054557
X-RAY DIFFRACTIONf_plane_restr0.008676
X-RAY DIFFRACTIONf_dihedral_angle_d16.1062247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.94-1.98850.32091390.2628264294
1.9885-2.04220.32081470.2419278999
2.0422-2.10230.27241440.2315277399
2.1023-2.17010.26821450.2314276699
2.1701-2.24760.31111340.2797253291
2.2476-2.33750.37041320.2997251290
2.3375-2.44370.29491480.2133280699
2.4437-2.57240.25681440.2088274299
2.5724-2.73330.2611470.2085277899
2.7333-2.94390.27461450.197276199
2.9439-3.23930.29891450.2026275099
3.2393-3.70610.23871460.1847276898
3.7061-4.66220.22291470.1554280099
4.6622-22.1470.16791470.1502279598

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