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- PDB-6srb: Crystal structure of glutathione transferase Omega 3C from Tramet... -

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Basic information

Entry
Database: PDB / ID: 6srb
TitleCrystal structure of glutathione transferase Omega 3C from Trametes versicolor
ComponentsUncharacterized protein
KeywordsTRANSFERASE / glutathione transferase
Function / homology
Function and homology information


: / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal ...: / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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 / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesTrametes pubescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSchwartz, M. / Favier, F. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LAS-0002-01 France
CitationJournal: Fungal Genet Biol. / Year: 2021
Title: Diversity of Omega Glutathione Transferases in mushroom-forming fungi revealed by phylogenetic, transcriptomic, biochemical and structural approaches.
Authors: Perrot, T. / Schwartz, M. / Deroy, A. / Girardet, J.M. / Kohler, A. / Morel-Rouhier, M. / Favier, F. / Gelhaye, E. / Didierjean, C.
History
DepositionSep 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2214
Polymers60,6072
Non-polymers6152
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-28 kcal/mol
Surface area20740 Å2
Unit cell
Length a, b, c (Å)132.480, 54.320, 75.190
Angle α, β, γ (deg.)90.000, 94.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein


Mass: 30303.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes pubescens (fungus) / Gene: TRAPUB_7610 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M2V359*PLUS
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 15% (w/v) polyethylene glycol 8000 and 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.65→47.894 Å / Num. obs: 59292 / % possible obs: 92.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 23.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.042 / Net I/σ(I): 14.59
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 4551 / CC1/2: 0.76 / Rrim(I) all: 0.55 / % possible all: 96.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HJS

6hjs


Resolution: 1.65→47.894 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.29
RfactorNum. reflection% reflection
Rfree0.2448 2963 5 %
Rwork0.2059 --
obs0.2079 59208 92.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.86 Å2 / Biso mean: 34.7027 Å2 / Biso min: 15.26 Å2
Refinement stepCycle: final / Resolution: 1.65→47.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 68 251 4050
Biso mean--29.71 35.94 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113881
X-RAY DIFFRACTIONf_angle_d1.085269
X-RAY DIFFRACTIONf_chiral_restr0.057552
X-RAY DIFFRACTIONf_plane_restr0.007680
X-RAY DIFFRACTIONf_dihedral_angle_d13.2082285
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.67710.31821460.2991276996
1.6771-1.7060.33551470.3043279096
1.706-1.7370.32641420.2703270195
1.737-1.77040.31391430.2581272795
1.7704-1.80660.26281500.2452283397
1.8066-1.84580.29571470.2459279497
1.8458-1.88880.30041470.2435280695
1.8888-1.9360.29431110.3038207772
1.936-1.98840.2751450.2322275395
1.9884-2.04690.31641440.2176272095
2.0469-2.11290.23771420.2145270793
2.1129-2.18850.27831480.2159281296
2.1885-2.27610.26541160.2437220476
2.2761-2.37970.24551430.2072271393
2.3797-2.50510.23551440.1978273594
2.5051-2.66210.23021390.1997265192
2.6621-2.86760.251450.1951274994
2.8676-3.15610.22481440.2084272894
3.1561-3.61270.24251410.1997269491
3.6127-4.5510.20531380.1672261388
4.551-47.8940.22411410.1866266988

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