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

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Basic information

Entry
Database: PDB / ID: 6sra
TitleCrystal structure of glutathione transferase Omega 2C from Trametes versicolor in complex with naringenin
Componentsglutathione transferase
KeywordsTRANSFERASE / glutathione transferase
Function / homology
Function and homology information


: / Glutathione S-transferase, N-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
R-naringenin / GLUTATHIONE / GST N-terminal domain-containing protein
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 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: glutathione transferase
B: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0166
Polymers54,8562
Non-polymers1,1594
Water82946
1
A: glutathione transferase
hetero molecules

A: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0166
Polymers54,8562
Non-polymers1,1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3180 Å2
ΔGint-25 kcal/mol
Surface area20800 Å2
MethodPISA
2
B: glutathione transferase
hetero molecules

B: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0166
Polymers54,8562
Non-polymers1,1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3200 Å2
ΔGint-24 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.891, 141.959, 65.309
Angle α, β, γ (deg.)90.000, 115.700, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein glutathione transferase


Mass: 27428.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor (turkey-tail 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
#3: Chemical ChemComp-CWE / R-naringenin


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
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: 0.97994 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97994 Å / Relative weight: 1
ReflectionResolution: 2.206→37.43 Å / Num. obs: 27025 / % possible obs: 96.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 33.16 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.076 / Rrim(I) all: 0.135 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.21-2.272.60.383607822990.8960.2660.4681.694
9.09-37.432.80.0911253950.980.0630.11110.895.6

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SR8

6sr8


Resolution: 2.206→34.369 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2
RfactorNum. reflection% reflection
Rfree0.2762 1327 4.92 %
Rwork0.2222 --
obs0.2249 26965 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.61 Å2 / Biso mean: 45.1599 Å2 / Biso min: 13.81 Å2
Refinement stepCycle: final / Resolution: 2.206→34.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 132 46 3864
Biso mean--35.89 28.85 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113878
X-RAY DIFFRACTIONf_angle_d1.2915273
X-RAY DIFFRACTIONf_chiral_restr0.076563
X-RAY DIFFRACTIONf_plane_restr0.01726
X-RAY DIFFRACTIONf_dihedral_angle_d16.2852311
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.206-2.29380.38061360.3155281695
2.2938-2.39820.31531450.2928289598
2.3982-2.52460.30881590.2612289998
2.5246-2.68270.3341360.2563288698
2.6827-2.88970.28591700.2451285397
2.8897-3.18030.33951360.2638285296
3.1803-3.64010.31530.2323277295
3.6401-4.58440.23481400.1927276893
4.5844-34.3690.21941520.1654289797

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