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- PDB-6gic: Crystal structure of glutathione transferase Omega 2S from Tramet... -

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Basic information

Entry
Database: PDB / ID: 6gic
TitleCrystal structure of glutathione transferase Omega 2S from Trametes versicolor in complex with oxyresveratrol
ComponentsGlutathione transferase Omega 2S
KeywordsTRANSFERASE / glutathione transferase / oxyresveratrol
Function / homology
Function and homology information


metal ion binding / cytoplasm
Similarity search - Function
: / 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
trans-oxyresveratrol / cis-oxyresveratrol / Glutathione S-transferase omega 2S
Similarity search - Component
Biological speciesTrametes versicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsSchwartz, M. / Favier, F. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LAS-0002-01 France
CitationJournal: ACS Sust Chem Eng / Year: 2018
Title: Fungal glutathione transferases as tools to explore the chemical diversity of Amazonian wood extractives
Authors: Perrot, T. / Schwartz, M. / Saiag, F. / Salzet, G. / Dumarcay, S. / Favier, F. / Gerardin, P. / Girardet, J.-M. / Sormani, R. / Morel-Rouhier, M. / Amusant, N. / Didierjean, C. / Gelhaye, E.
History
DepositionMay 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione transferase Omega 2S
B: Glutathione transferase Omega 2S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1695
Polymers54,6562
Non-polymers5133
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-13 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.612, 93.903, 95.800
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 Glutathione transferase Omega 2S


Mass: 27328.105 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: A0A452CSY5*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EZE / trans-oxyresveratrol


Mass: 244.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O4
#4: Chemical ChemComp-EZH / cis-oxyresveratrol


Mass: 244.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10.7% PEG4000, 0.1 M pH 7.0 HEPES-MES buffer (in the ratio 4:6, respectively), 0.05 M sodium acetate and 0.05 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97955 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 2.3→47.9 Å / Num. obs: 24016 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.8
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.76 / Num. unique obs: 3819 / % possible all: 99.9

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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: 2.304→47.9 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.13
RfactorNum. reflection% reflection
Rfree0.2524 1200 5 %
Rwork0.1925 --
obs0.1955 24014 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.304→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 37 101 3779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113790
X-RAY DIFFRACTIONf_angle_d1.1075157
X-RAY DIFFRACTIONf_dihedral_angle_d17.4152289
X-RAY DIFFRACTIONf_chiral_restr0.05548
X-RAY DIFFRACTIONf_plane_restr0.008715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3041-2.39630.3321300.24182483X-RAY DIFFRACTION100
2.3963-2.50540.27261310.22282485X-RAY DIFFRACTION100
2.5054-2.63750.29081320.21582499X-RAY DIFFRACTION100
2.6375-2.80270.30321330.21112522X-RAY DIFFRACTION100
2.8027-3.01910.28621310.22412495X-RAY DIFFRACTION100
3.0191-3.32280.26541320.21582519X-RAY DIFFRACTION100
3.3228-3.80350.2661340.18592544X-RAY DIFFRACTION100
3.8035-4.79130.22491350.15822579X-RAY DIFFRACTION100
4.7913-47.91030.18421420.16722688X-RAY DIFFRACTION100

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