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- PDB-6hjs: Crystal structure of glutathione transferase Omega 1C from Tramet... -

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Basic information

Entry
Database: PDB / ID: 6hjs
TitleCrystal structure of glutathione transferase Omega 1C from Trametes versicolor
ComponentsUncharacterized protein
KeywordsTRANSFERASE / glutathione transferase
Function / homology
Function and homology information


: / 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 FP-101664 SS1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.612 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. / Fa Vier, F. / Gelhaye, E. / Didierjean, C.
History
DepositionSep 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: 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 1.2Jan 17, 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)54,4246
Polymers53,3322
Non-polymers1,0914
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-15 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.685, 86.442, 92.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 26666.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor FP-101664 SS1 (fungus)
Gene: TRAVEDRAFT_157166 / Production host: Escherichia coli (E. coli) / References: UniProt: R7S6N2
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% (w/v) polyethylene glycol 8000 in 0.1 M pH 7.5 HEPES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98014 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98014 Å / Relative weight: 1
ReflectionResolution: 1.61→46.05 Å / Num. obs: 65189 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 15.4
Reflection shellResolution: 1.61→1.64 Å / Rmerge(I) obs: 0.596 / Rpim(I) all: 0.247 / Rrim(I) all: 0.646

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Processing

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

6f43


Resolution: 1.612→43.221 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.92
RfactorNum. reflection% reflection
Rfree0.2116 3408 5.23 %
Rwork0.1863 --
obs0.1877 65108 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.612→43.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 70 465 4197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073834
X-RAY DIFFRACTIONf_angle_d0.8795208
X-RAY DIFFRACTIONf_dihedral_angle_d14.4712286
X-RAY DIFFRACTIONf_chiral_restr0.052562
X-RAY DIFFRACTIONf_plane_restr0.007672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6123-1.63530.29211210.24152486X-RAY DIFFRACTION97
1.6353-1.65970.24141400.20482558X-RAY DIFFRACTION100
1.6597-1.68570.23651450.19442503X-RAY DIFFRACTION100
1.6857-1.71330.22991450.1972537X-RAY DIFFRACTION100
1.7133-1.74290.26511400.2012583X-RAY DIFFRACTION100
1.7429-1.77460.22671100.20672553X-RAY DIFFRACTION100
1.7746-1.80870.25471260.20862556X-RAY DIFFRACTION100
1.8087-1.84560.23381330.20372557X-RAY DIFFRACTION100
1.8456-1.88570.23521420.19862560X-RAY DIFFRACTION100
1.8857-1.92960.26031360.1962528X-RAY DIFFRACTION100
1.9296-1.97790.23351630.19312554X-RAY DIFFRACTION100
1.9779-2.03130.22261570.1932528X-RAY DIFFRACTION100
2.0313-2.09110.19851510.18752562X-RAY DIFFRACTION100
2.0911-2.15860.22091480.18692541X-RAY DIFFRACTION100
2.1586-2.23570.23431710.18942545X-RAY DIFFRACTION100
2.2357-2.32530.22691660.19182547X-RAY DIFFRACTION100
2.3253-2.43110.20791150.18232601X-RAY DIFFRACTION100
2.4311-2.55920.22511110.19292596X-RAY DIFFRACTION100
2.5592-2.71960.23061370.19512603X-RAY DIFFRACTION100
2.7196-2.92950.23631290.19862583X-RAY DIFFRACTION100
2.9295-3.22420.20971470.19372607X-RAY DIFFRACTION100
3.2242-3.69050.19851500.17962626X-RAY DIFFRACTION100
3.6905-4.64880.15851580.15712629X-RAY DIFFRACTION100
4.6488-43.23650.17111670.16222757X-RAY DIFFRACTION100

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