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- PDB-6f4f: Crystal structure of glutathione transferase Omega 3S from Tramet... -

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Basic information

Entry
Database: PDB / ID: 6f4f
TitleCrystal structure of glutathione transferase Omega 3S from Trametes versicolor in complex with glutathionyl-S-dinitrobenzene
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
GLUTATHIONE S-(2,4 DINITROBENZENE) / DI(HYDROXYETHYL)ETHER / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

Downloads & links

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Assembly

Deposited unit
A: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4369
Polymers55,0532
Non-polymers1,3837
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-28 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.430, 103.720, 107.320
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 (turkey-tail fungus)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E145*PLUS

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Non-polymers , 5 types, 458 molecules

#2: Chemical ChemComp-GDN / GLUTATHIONE S-(2,4 DINITROBENZENE)


Mass: 473.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N5O10S
#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.: 451 / 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: 51.75 %
Crystal growTemperature: 278 K / Method: microbatch
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: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→41.78 Å / Num. obs: 56918 / % possible obs: 98.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.2
Reflection shellResolution: 1.75→1.8 Å

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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: 6F43

6f43


Resolution: 1.75→37.291 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 2845 5 %
Rwork0.1631 --
obs0.1652 56897 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→37.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 91 451 4338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134024
X-RAY DIFFRACTIONf_angle_d1.3425478
X-RAY DIFFRACTIONf_dihedral_angle_d17.1252405
X-RAY DIFFRACTIONf_chiral_restr0.215581
X-RAY DIFFRACTIONf_plane_restr0.01722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78010.34641400.29812668X-RAY DIFFRACTION100
1.7801-1.81250.30211400.27432655X-RAY DIFFRACTION99
1.8125-1.84740.27321420.25322696X-RAY DIFFRACTION100
1.8474-1.88510.24691400.22382674X-RAY DIFFRACTION99
1.8851-1.92610.31981420.21022691X-RAY DIFFRACTION100
1.9261-1.97090.2381410.20442670X-RAY DIFFRACTION99
1.9709-2.02020.22461440.18822733X-RAY DIFFRACTION99
2.0202-2.07480.25661400.19232663X-RAY DIFFRACTION99
2.0748-2.13580.2021410.17252695X-RAY DIFFRACTION99
2.1358-2.20480.23451420.15572692X-RAY DIFFRACTION99
2.2048-2.28350.17421420.14992695X-RAY DIFFRACTION99
2.2835-2.3750.19811420.15042696X-RAY DIFFRACTION99
2.375-2.4830.19741410.14822682X-RAY DIFFRACTION99
2.483-2.61390.1881430.14652720X-RAY DIFFRACTION99
2.6139-2.77760.191440.13752723X-RAY DIFFRACTION99
2.7776-2.9920.16031420.14562713X-RAY DIFFRACTION99
2.992-3.29290.20721440.1532723X-RAY DIFFRACTION99
3.2929-3.7690.19751430.14822723X-RAY DIFFRACTION99
3.769-4.74710.17521440.13052733X-RAY DIFFRACTION97
4.7471-37.29910.20241480.16742807X-RAY DIFFRACTION95

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