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- PDB-6ep6: ARABIDOPSIS THALIANA GSTU23, reduced -

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Basic information

Entry
Database: PDB / ID: 6ep6
TitleARABIDOPSIS THALIANA GSTU23, reduced
ComponentsGlutathione S-transferase U23
KeywordsTRANSFERASE / TAU CLASS / PEROXIDASE
Function / homology
Function and homology information


toxin catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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 S-transferase U23
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.592 Å
AuthorsTossounian, M.A. / Van Molle, I. / Wahni, K. / Jacques, S. / Vertommen, D. / Gevaert, K. / Van Breusegem, F. / Young, D. / Rosado, L. / Messens, J.
Funding support Belgium, 4items
OrganizationGrant numberCountry
FWOG0D7914N Belgium
VIB Marie Curie COFUND Belgium
Hercules FoundationHERC16 Belgium
VUBSRP34 Belgium
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Disulfide bond formation protects Arabidopsis thaliana glutathione transferase tau 23 from oxidative damage.
Authors: Tossounian, M.A. / Van Molle, I. / Wahni, K. / Jacques, S. / Gevaert, K. / Van Breusegem, F. / Vertommen, D. / Young, D. / Rosado, L.A. / Messens, J.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase U23
B: Glutathione S-transferase U23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7507
Polymers51,4252
Non-polymers3255
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-34 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.597, 50.449, 113.702
Angle α, β, γ (deg.)90.00, 108.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-490-

HOH

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Components

#1: Protein Glutathione S-transferase U23 / AtGSTU23 / GST class-tau member 23


Mass: 25712.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSTU23, At1g78320, F3F9.14 / Plasmid: PDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q9M9F1, glutathione transferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 0.16 M MGCL2, 0.08 M TRIS PH 8.5, 24% PEG4000, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2015 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 64020 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Biso Wilson estimate: 22.28 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.16
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 3.02 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VO4

2vo4


Resolution: 1.592→44.179 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 3122 5 %
Rwork0.1888 --
obs0.1904 62435 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.592→44.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 20 311 3776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063587
X-RAY DIFFRACTIONf_angle_d1.0024870
X-RAY DIFFRACTIONf_dihedral_angle_d12.11331
X-RAY DIFFRACTIONf_chiral_restr0.041528
X-RAY DIFFRACTIONf_plane_restr0.005611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5917-1.61650.38991150.3952184X-RAY DIFFRACTION81
1.6165-1.6430.38011420.32632696X-RAY DIFFRACTION97
1.643-1.67140.34771390.31572645X-RAY DIFFRACTION97
1.6714-1.70180.33141420.31512692X-RAY DIFFRACTION97
1.7018-1.73450.34541400.30982660X-RAY DIFFRACTION97
1.7345-1.76990.34361410.30722679X-RAY DIFFRACTION98
1.7699-1.80840.33031430.29522700X-RAY DIFFRACTION97
1.8084-1.85050.38541390.28932672X-RAY DIFFRACTION98
1.8505-1.89670.30131420.25992693X-RAY DIFFRACTION98
1.8967-1.9480.27461440.24052727X-RAY DIFFRACTION98
1.948-2.00530.23191420.20782705X-RAY DIFFRACTION99
2.0053-2.07010.22181420.19032698X-RAY DIFFRACTION98
2.0701-2.14410.21511450.17552742X-RAY DIFFRACTION99
2.1441-2.22990.21251430.16532718X-RAY DIFFRACTION99
2.2299-2.33140.22841440.16422741X-RAY DIFFRACTION99
2.3314-2.45430.19161420.17212703X-RAY DIFFRACTION98
2.4543-2.6080.19921440.18182729X-RAY DIFFRACTION99
2.608-2.80940.19961460.1762781X-RAY DIFFRACTION99
2.8094-3.0920.20851450.18252740X-RAY DIFFRACTION99
3.092-3.53930.22611460.16852785X-RAY DIFFRACTION99
3.5393-4.45840.17881470.15032781X-RAY DIFFRACTION99
4.4584-44.19630.17031490.1672842X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5102-0.12370.2761.06660.10321.8529-0.0299-0.08560.03030.09520.0122-0.0861-0.060.11950.01330.1171-0.0028-0.01570.1470.02180.120530.121545.8088256.4875
21.05860.2657-0.06511.354-0.43781.8669-0.03530.06710.0358-0.12430.02620.0852-0.0001-0.11010.0120.11990.0059-0.01470.1372-0.03190.12827.824744.5524228.6186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 4:213)
2X-RAY DIFFRACTION2(chain B and resseq 4:219)

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