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- PDB-6f43: Crystal structure of apo form of Glutathione transferase Omega 3S... -

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Basic information

Entry
Database: PDB / ID: 6f43
TitleCrystal structure of apo form of Glutathione transferase Omega 3S from Trametes versicolor
Componentsglutathione transferase
KeywordsTRANSFERASE / Glutathione / fungi / polyphenols / wood decayers
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / metal ion binding / cytoplasm
Similarity search - Function
: / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSchwartz, M. / Favier, F. / Didierjean, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LABX-0002-01 France
CNRS-University of LorrainePEPS MIRABELLE 2016 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
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)55,72611
Polymers55,0532
Non-polymers6739
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-18 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.480, 104.520, 107.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein glutathione transferase


Mass: 27526.504 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: A0A384E145*PLUS, glutathione transferase

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Non-polymers , 5 types, 488 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.58 Å3/Da / Density % sol: 52.34 % / Description: Bipyramidal crystals.
Crystal growTemperature: 278 K / Method: microbatch / pH: 4.5
Details: 30 % PEG 400, 0.2 M Calcium Acetate, 0.1 M Acetate Buffer, pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→47.88 Å / Num. obs: 125602 / % possible obs: 100 % / Redundancy: 8.2 % / Rsym value: 0.071 / Net I/σ(I): 16.5
Reflection shellResolution: 1.35→1.39 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PQI

4pqi


Resolution: 1.35→47.877 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1679 6280 5 %
Rwork0.1366 --
obs0.1381 125557 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→47.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 43 479 4318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133957
X-RAY DIFFRACTIONf_angle_d1.2425379
X-RAY DIFFRACTIONf_dihedral_angle_d21.2581465
X-RAY DIFFRACTIONf_chiral_restr0.089573
X-RAY DIFFRACTIONf_plane_restr0.01708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.3032100.25193988X-RAY DIFFRACTION100
1.3653-1.38140.28092060.23343901X-RAY DIFFRACTION100
1.3814-1.39830.26142070.2043946X-RAY DIFFRACTION100
1.3983-1.4160.20162070.19333931X-RAY DIFFRACTION100
1.416-1.43460.23032060.18653911X-RAY DIFFRACTION100
1.4346-1.45420.23412070.17553939X-RAY DIFFRACTION100
1.4542-1.4750.19372070.16083924X-RAY DIFFRACTION100
1.475-1.4970.19882070.15263937X-RAY DIFFRACTION100
1.497-1.52040.16582080.1513941X-RAY DIFFRACTION100
1.5204-1.54540.17682080.1363956X-RAY DIFFRACTION100
1.5454-1.5720.15832070.12733944X-RAY DIFFRACTION100
1.572-1.60060.14672060.12253913X-RAY DIFFRACTION100
1.6006-1.63140.14692110.11534002X-RAY DIFFRACTION100
1.6314-1.66470.15372060.10913906X-RAY DIFFRACTION100
1.6647-1.70090.14762080.11233955X-RAY DIFFRACTION100
1.7009-1.74040.13952090.10923981X-RAY DIFFRACTION100
1.7404-1.7840.16362070.11473924X-RAY DIFFRACTION100
1.784-1.83220.15632090.11213974X-RAY DIFFRACTION100
1.8322-1.88610.13542090.1153972X-RAY DIFFRACTION100
1.8861-1.9470.15282090.11873973X-RAY DIFFRACTION100
1.947-2.01660.15542090.12113969X-RAY DIFFRACTION100
2.0166-2.09730.15532100.12593992X-RAY DIFFRACTION100
2.0973-2.19280.15932100.1263980X-RAY DIFFRACTION100
2.1928-2.30840.15822100.12044000X-RAY DIFFRACTION100
2.3084-2.4530.15272100.12363984X-RAY DIFFRACTION100
2.453-2.64240.1542120.12864040X-RAY DIFFRACTION100
2.6424-2.90830.17052120.13194019X-RAY DIFFRACTION100
2.9083-3.3290.16712130.14434049X-RAY DIFFRACTION100
3.329-4.19390.15882160.13654113X-RAY DIFFRACTION100
4.1939-47.90720.19012240.15774213X-RAY DIFFRACTION99

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