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- PDB-6ht6: Crystal structure of glutathione transferase Omega 2S from Tramet... -

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Basic information

Entry
Database: PDB / ID: 6ht6
TitleCrystal structure of glutathione transferase Omega 2S from Trametes versicolor in complex with 2,4-dihydroxybenzophenone
ComponentsGlutathione S-transferase omega 2S
KeywordsTRANSFERASE / glutathione transferase
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
[2,4-bis(oxidanyl)phenyl]-phenyl-methanone / Glutathione S-transferase omega 2S
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.671 Å
AuthorsSchwartz, M. / Favier, F. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LAS-0002-01 France
CitationJournal: Sci Rep / Year: 2018
Title: Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor.
Authors: Schwartz, M. / Perrot, T. / Aubert, E. / Dumarcay, S. / Favier, F. / Gerardin, P. / Morel-Rouhier, M. / Mulliert, G. / Saiag, F. / Didierjean, C. / Gelhaye, E.
History
DepositionOct 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / 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 / _entity.formula_weight / _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 S-transferase omega 2S
B: Glutathione S-transferase omega 2S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1095
Polymers54,6562
Non-polymers4533
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-12 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.999, 93.128, 95.548
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 S-transferase omega 2S


Mass: 27328.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor (turkey-tail fungus)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSY5*PLUS
#2: Chemical ChemComp-CUT / [2,4-bis(oxidanyl)phenyl]-phenyl-methanone


Mass: 214.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97951 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: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.67→47.774 Å / Num. obs: 15526 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.055 / Rrim(I) all: 0.148 / Net I/σ(I): 11.9
Reflection shellResolution: 2.67→2.8 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.2 / Rpim(I) all: 0.245 / Rrim(I) all: 0.666 / % possible all: 99.1

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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: 6GIB

6gib


Resolution: 2.671→47.774 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2841 818 5.29 %
Rwork0.2207 --
obs0.224 15450 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.671→47.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 33 16 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123740
X-RAY DIFFRACTIONf_angle_d1.3075090
X-RAY DIFFRACTIONf_dihedral_angle_d17.4912227
X-RAY DIFFRACTIONf_chiral_restr0.068541
X-RAY DIFFRACTIONf_plane_restr0.011671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6706-2.83790.3151320.24782372X-RAY DIFFRACTION99
2.8379-3.0570.32451530.24932373X-RAY DIFFRACTION100
3.057-3.36460.31051200.22862417X-RAY DIFFRACTION100
3.3646-3.85130.33571480.24672418X-RAY DIFFRACTION99
3.8513-4.85150.2521150.19272483X-RAY DIFFRACTION100
4.8515-47.78160.23161500.20242569X-RAY DIFFRACTION100

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