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- PDB-6gcc: Crystal structure of glutathione transferase Xi 3 mutant C56S fro... -

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Basic information

Entry
Database: PDB / ID: 6gcc
TitleCrystal structure of glutathione transferase Xi 3 mutant C56S from Trametes versicolor in complex with dextran-sulfate
ComponentsGlutathione transferase Xi 3 mutant C56S
KeywordsTRANSFERASE / glutathione transferase
Function / homology
Function and homology information


glutathione transferase activity / cytoplasm
Similarity search - Function
Glutathione S-transferase Omega/GSH / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...Glutathione S-transferase Omega/GSH / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutathione transferase Xi 3 mutant C56S
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchwartz, M. / Favier, F. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LAS-0002-01 France
CitationJournal: FEBS Lett. / Year: 2018
Title: Trametes versicolor glutathione transferase Xi 3, a dual Cys-GST with catalytic specificities of both Xi and Omega classes.
Authors: Schwartz, M. / Perrot, T. / Deroy, A. / Roret, T. / Morel-Rouhier, M. / Mulliert, G. / Gelhaye, E. / Favier, F. / Didierjean, C.
History
DepositionApr 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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: Glutathione transferase Xi 3 mutant C56S
B: Glutathione transferase Xi 3 mutant C56S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5844
Polymers74,2942
Non-polymers2,2902
Water13,187732
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-12 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.256, 72.256, 317.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glutathione transferase Xi 3 mutant C56S


Mass: 37147.082 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: A0A3F2YM29*PLUS
#2: Polysaccharide 3,4-di-O-sulfo-alpha-D-glucopyranose-(1-6)-3,4-di-O-sulfo-alpha-D-altropyranose-(1-6)-1,2,3,4-tetra- ...3,4-di-O-sulfo-alpha-D-glucopyranose-(1-6)-3,4-di-O-sulfo-alpha-D-altropyranose-(1-6)-1,2,3,4-tetra-O-sulfo-alpha-D-allopyranose


Type: oligosaccharide / Mass: 1144.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2222h-1a_1-5_1*OSO/3=O/3=O_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O][a1222h-1a_1-5_3*OSO/3=O/3=O_4*OSO/3=O/3=O][a2122h-1a_1-5_3*OSO/3=O/3=O_4*OSO/3=O/3=O]/1-2-3/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][<O3S1>]{[(1+1)][a-D-Allp1SO32SO33SO34SO3]{[(6+1)][a-D-Altp3SO34SO3]{[(6+1)][a-D-Glcp3SO34SO3]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5
Details: 20% (w/v) polyethylene glycol 8,000, 0.1M pH 6.5 sodium cacodylate buffer and 0.2M magnesium acetate, dextran-sulfate as additive

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97977 Å / Relative weight: 1
ReflectionResolution: 1.9→46.01 Å / Num. obs: 65928 / % possible obs: 97.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.25 / Num. unique obs: 3578

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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: 6GCA

6gca


Resolution: 1.9→46.01 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 3340 5.1 %
Rwork0.16 --
obs0.162 65516 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4724 0 132 732 5588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115017
X-RAY DIFFRACTIONf_angle_d1.366874
X-RAY DIFFRACTIONf_dihedral_angle_d15.9972890
X-RAY DIFFRACTIONf_chiral_restr0.068750
X-RAY DIFFRACTIONf_plane_restr0.008854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.92820.3771030.40332128X-RAY DIFFRACTION82
1.9282-1.9570.28891260.25232382X-RAY DIFFRACTION91
1.957-1.98750.23731410.20322500X-RAY DIFFRACTION96
1.9875-2.02010.2231550.18752586X-RAY DIFFRACTION99
2.0201-2.0550.21661430.16372621X-RAY DIFFRACTION100
2.055-2.09230.20851060.15772638X-RAY DIFFRACTION100
2.0923-2.13260.17391460.1562637X-RAY DIFFRACTION99
2.1326-2.17610.21031240.16082633X-RAY DIFFRACTION100
2.1761-2.22340.231250.17382616X-RAY DIFFRACTION99
2.2234-2.27510.36021370.30962358X-RAY DIFFRACTION90
2.2751-2.3320.19341410.1552638X-RAY DIFFRACTION100
2.332-2.39510.1911570.14382596X-RAY DIFFRACTION100
2.3951-2.46550.14631390.13942631X-RAY DIFFRACTION99
2.4655-2.54510.20051420.1382650X-RAY DIFFRACTION100
2.5451-2.63610.18081450.13752639X-RAY DIFFRACTION99
2.6361-2.74160.18671410.1442652X-RAY DIFFRACTION99
2.7416-2.86640.1831490.152646X-RAY DIFFRACTION99
2.8664-3.01750.16761330.14992658X-RAY DIFFRACTION98
3.0175-3.20650.19661580.15792635X-RAY DIFFRACTION99
3.2065-3.4540.18861390.14822642X-RAY DIFFRACTION98
3.454-3.80140.17461590.15032623X-RAY DIFFRACTION97
3.8014-4.35110.18141340.12592666X-RAY DIFFRACTION97
4.3511-5.48050.13781440.12632673X-RAY DIFFRACTION96
5.4805-46.02760.18331530.16912728X-RAY DIFFRACTION91

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