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- PDB-6ep7: ARABIDOPSIS THALIANA GSTU23, GSH bound -

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Basic information

Entry
Database: PDB / ID: 6ep7
TitleARABIDOPSIS THALIANA GSTU23, GSH bound
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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like ...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 / Soluble glutathione S-transferase N-terminal domain profile. / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase U23
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.947 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 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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)52,4339
Polymers51,4252
Non-polymers1,0077
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-32 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.070, 50.645, 113.518
Angle α, β, γ (deg.)90.00, 108.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-433-

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-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / 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: 2.36 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.947→30 Å / Num. obs: 35062 / % possible obs: 94.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 22.42 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.93 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 6EP6

6ep6


Resolution: 1.947→28.842 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1657 5 %
Rwork0.1648 --
obs0.167 33149 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.947→28.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 65 311 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073609
X-RAY DIFFRACTIONf_angle_d0.984894
X-RAY DIFFRACTIONf_dihedral_angle_d12.9691340
X-RAY DIFFRACTIONf_chiral_restr0.044528
X-RAY DIFFRACTIONf_plane_restr0.005617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9468-2.00410.27841130.21932150X-RAY DIFFRACTION78
2.0041-2.06870.26691350.1892555X-RAY DIFFRACTION94
2.0687-2.14270.2121370.17722617X-RAY DIFFRACTION94
2.1427-2.22840.21221370.17082598X-RAY DIFFRACTION95
2.2284-2.32980.22021390.17052632X-RAY DIFFRACTION95
2.3298-2.45260.22621400.17312666X-RAY DIFFRACTION96
2.4526-2.60610.21021390.1722634X-RAY DIFFRACTION96
2.6061-2.80720.21721420.17222713X-RAY DIFFRACTION96
2.8072-3.08940.23121410.18032683X-RAY DIFFRACTION98
3.0894-3.53580.21251440.15992743X-RAY DIFFRACTION98
3.5358-4.4520.17931440.13822737X-RAY DIFFRACTION98
4.452-28.84560.18761460.15762764X-RAY DIFFRACTION96
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)
12.11760.1352-0.72221.36950.15742.75650.00730.27650.0186-0.1191-0.05510.1602-0.0823-0.35040.0190.09580.028-0.03680.1813-0.030.14-3.993737.9397-202.2957
21.5614-0.2233-0.6831.38470.7773.3489-0.0829-0.1495-0.0070.18630.0138-0.07260.02080.32430.05830.18670.0071-0.01010.14280.04740.1343-1.683136.8435-174.4522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 4:213)
2X-RAY DIFFRACTION2(chain B and resseq 4:217)

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