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- PDB-5ey6: CRYSTAL STRUCTURE OF GLUTATHIONE TRANSFERASE F2 FROM POPULUS TRIC... -

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Basic information

Entry
Database: PDB / ID: 5ey6
TitleCRYSTAL STRUCTURE OF GLUTATHIONE TRANSFERASE F2 FROM POPULUS TRICHOCARPA
ComponentsPhi class glutathione transferase GSTF2
KeywordsTRANSFERASE / glutathione / ligandin
Function / homology
Function and homology information


glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / response to toxic substance / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione transferase
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDidierjean, C. / Rouhier, N. / Pegeot, H. / Gense, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LABX-0002-01 France
CitationJournal: FEBS J. / Year: 2017
Title: Structural plasticity among glutathione transferase Phi members: natural combination of catalytic residues confers dual biochemical activities.
Authors: Pegeot, H. / Mathiot, S. / Perrot, T. / Gense, F. / Hecker, A. / Didierjean, C. / Rouhier, N.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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: Phi class glutathione transferase GSTF2
B: Phi class glutathione transferase GSTF2


Theoretical massNumber of molelcules
Total (without water)49,0352
Polymers49,0352
Non-polymers00
Water7,206400
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-12 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.383, 83.316, 60.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-433-

HOH

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Components

#1: Protein Phi class glutathione transferase GSTF2 / Uncharacterized protein


Mass: 24517.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_0002s01660g / Production host: Escherichia coli (E. coli) / References: UniProt: B9GQ64, glutathione transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5 / Details: 30% PEG MME 2000, 0.1 M Na acetate, Na MES pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.997967 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997967 Å / Relative weight: 1
ReflectionResolution: 1.9→48.72 Å / Num. obs: 38738 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RI6

4ri6


Resolution: 1.9→41.658 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1850 4.78 %Random selection
Rwork0.1931 ---
obs0.1948 38686 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→41.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 0 400 3844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063547
X-RAY DIFFRACTIONf_angle_d0.9774798
X-RAY DIFFRACTIONf_dihedral_angle_d13.051343
X-RAY DIFFRACTIONf_chiral_restr0.037504
X-RAY DIFFRACTIONf_plane_restr0.005632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.30341380.25132768X-RAY DIFFRACTION99
1.9514-2.00880.27561390.24842773X-RAY DIFFRACTION99
2.0088-2.07360.26941410.23892787X-RAY DIFFRACTION100
2.0736-2.14770.25231410.22252800X-RAY DIFFRACTION99
2.1477-2.23370.27371410.22212819X-RAY DIFFRACTION100
2.2337-2.33540.26961390.20942787X-RAY DIFFRACTION100
2.3354-2.45850.21021410.1992802X-RAY DIFFRACTION100
2.4585-2.61250.25161430.20552850X-RAY DIFFRACTION100
2.6125-2.81420.21881410.20652810X-RAY DIFFRACTION100
2.8142-3.09730.25821430.19952850X-RAY DIFFRACTION100
3.0973-3.54530.18421450.18362888X-RAY DIFFRACTION100
3.5453-4.46580.18271440.15922880X-RAY DIFFRACTION100
4.4658-41.6680.22591540.16763022X-RAY DIFFRACTION99

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