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- PDB-6gca: Crystal structure of glutathione transferase Xi 3 from Trametes v... -

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Basic information

Entry
Database: PDB / ID: 6gca
TitleCrystal structure of glutathione transferase Xi 3 from Trametes versicolor
ComponentsGlutathione transferase Xi 3 from Trametes versicolor
KeywordsTRANSFERASE / glutathione transferase
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase Omega/GSH / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione transferase Xi 3 from Trametes versicolor
Similarity search - Component
Biological speciesTrametes versicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.282 Å
AuthorsSchwartz, M. / Favier, F. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LAS-0002-01 France
CitationJournal: FEBS Lett. / Year: 2018
Title: Trametes versicolor glutathione transferase Xi 3, a dual Cys-GST with catalytic specificities of both Xi and Omega classes.
Authors: Schwartz, M. / Perrot, T. / Deroy, A. / Roret, T. / Morel-Rouhier, M. / Mulliert, G. / Gelhaye, E. / Favier, F. / Didierjean, C.
History
DepositionApr 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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: Glutathione transferase Xi 3 from Trametes versicolor
B: Glutathione transferase Xi 3 from Trametes versicolor


Theoretical massNumber of molelcules
Total (without water)74,3262
Polymers74,3262
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.370, 57.460, 94.560
Angle α, β, γ (deg.)90.00, 107.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutathione transferase Xi 3 from Trametes versicolor


Mass: 37163.148 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: A0A3F2YM27*PLUS, glutathione transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5
Details: 20% (w/v) polyethylene glycol 8,000, 0.1M pH 6.5 sodium cacodylate buffer and 0.2M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97974 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97974 Å / Relative weight: 1
ReflectionResolution: 2.28→48.68 Å / Num. obs: 33851 / % possible obs: 98.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 2.28→2.34 Å / Rmerge(I) obs: 0.69 / Num. unique all: 2465

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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: 3PPU

3ppu


Resolution: 2.282→36.433 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1656 4.89 %
Rwork0.1643 --
obs0.1675 33840 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.282→36.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4837 0 0 355 5192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124985
X-RAY DIFFRACTIONf_angle_d1.096792
X-RAY DIFFRACTIONf_dihedral_angle_d15.0042923
X-RAY DIFFRACTIONf_chiral_restr0.058729
X-RAY DIFFRACTIONf_plane_restr0.007872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2817-2.34880.35671210.25192674X-RAY DIFFRACTION98
2.3488-2.42460.27491410.19162685X-RAY DIFFRACTION100
2.4246-2.51130.28911500.19442732X-RAY DIFFRACTION100
2.5113-2.61180.2511480.19582714X-RAY DIFFRACTION100
2.6118-2.73060.26631500.18872669X-RAY DIFFRACTION100
2.7306-2.87450.25761460.19062699X-RAY DIFFRACTION100
2.8745-3.05460.25881480.17632708X-RAY DIFFRACTION100
3.0546-3.29030.25151340.18212720X-RAY DIFFRACTION100
3.2903-3.62110.23781270.16222733X-RAY DIFFRACTION99
3.6211-4.14450.21571070.14292309X-RAY DIFFRACTION83
4.1445-5.21910.16481440.11812751X-RAY DIFFRACTION100
5.2191-36.4380.16141400.13382790X-RAY DIFFRACTION99

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