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- PDB-6f01: ARABIDOPSIS THALIANA GSTF9, GSO3 AND GSOH BOUND -

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Basic information

Entry
Database: PDB / ID: 6f01
TitleARABIDOPSIS THALIANA GSTF9, GSO3 AND GSOH BOUND
ComponentsGlutathione S-transferase F9
KeywordsTRANSFERASE / PHI CLASS / PEROXIDASE / GSO3 / GSOH
Function / homology
Function and homology information


salicylic acid binding / toxin catabolic process / glutathione binding / apoplast / plasmodesma / plant-type vacuole / thylakoid / glutathione peroxidase activity / chloroplast stroma / response to zinc ion ...salicylic acid binding / toxin catabolic process / glutathione binding / apoplast / plasmodesma / plant-type vacuole / thylakoid / glutathione peroxidase activity / chloroplast stroma / response to zinc ion / glutathione transferase / glutathione transferase activity / response to cadmium ion / chloroplast / defense response / peroxisome / copper ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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
BROMIDE ION / S-Hydroxy-Glutathione / GLUTATHIONE SULFONIC ACID / Glutathione S-transferase F9
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTossounian, M.A. / Wahni, K. / Van Molle, I. / Vertommen, D. / Rosado, L. / Messens, J.
Funding support Belgium, 5items
OrganizationGrant numberCountry
FWO Belgium
FWOG0D7914N Belgium
VIB-Marie Curie Cofund Belgium
VUBSRP34 Belgium
HerculesHERC16 Belgium
CitationJournal: Protein Sci. / Year: 2019
Title: Redox-regulated methionine oxidation of Arabidopsis thaliana glutathione transferase Phi9 induces H-site flexibility.
Authors: Tossounian, M.A. / Wahni, K. / Van Molle, I. / Vertommen, D. / Astolfi Rosado, L. / Messens, J.
History
DepositionNov 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 1, 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 S-transferase F9
B: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3788
Polymers48,3562
Non-polymers1,0236
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-17 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.760, 114.760, 90.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione S-transferase F9 / GLUTATHIONE-S-TRANSFERASE PHI9 / AtGSTF9 / AtGSTF7 / GST class-phi member 9


Mass: 24177.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSTF9, GLUTTR, GSTF7, At2g30860, F7F1.7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O80852, glutathione transferase

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Non-polymers , 5 types, 167 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O9S
#5: Chemical ChemComp-GS8 / S-Hydroxy-Glutathione


Mass: 323.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O7S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: 0.1M KBr 30% PEGMME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 29, 2015 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→66.84 Å / Num. obs: 24179 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Biso Wilson estimate: 40.02 Å2 / Rmerge(I) obs: 0.177 / Net I/σ(I): 11.56
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 2.09 / % possible all: 99.9

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Processing

Software
NameClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GSTF9

Resolution: 2.5→66.837 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.21
RfactorNum. reflection% reflection
Rfree0.2089 1195 4.9 %
Rwork0.1643 --
obs0.1666 24119 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→66.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 58 161 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013413
X-RAY DIFFRACTIONf_angle_d1.2684646
X-RAY DIFFRACTIONf_dihedral_angle_d13.3871219
X-RAY DIFFRACTIONf_chiral_restr0.05515
X-RAY DIFFRACTIONf_plane_restr0.007588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60010.34691320.26382526X-RAY DIFFRACTION100
2.6001-2.71840.25021520.21312490X-RAY DIFFRACTION100
2.7184-2.86180.25261350.19772521X-RAY DIFFRACTION100
2.8618-3.04110.24761330.18982515X-RAY DIFFRACTION100
3.0411-3.27590.23781180.17762541X-RAY DIFFRACTION100
3.2759-3.60550.21871260.15882543X-RAY DIFFRACTION100
3.6055-4.12720.18841460.1462539X-RAY DIFFRACTION100
4.1272-5.19950.15441170.12672597X-RAY DIFFRACTION100
5.1995-66.86130.19031360.15822652X-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)
11.43570.2083-0.73271.4194-0.40393.8861-0.0995-0.0437-0.07650.02260.102-0.070.26380.10950.00160.2766-0.0694-0.04080.2523-0.00190.2869-41.043139.412-11.7758
22.07910.4186-0.1031.26690.23033.2818-0.0118-0.05410.2494-0.08050.08-0.0316-0.47060.0457-0.05840.3093-0.0431-0.01150.2378-0.00560.3386-42.584261.4817-4.9199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 2:213)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 2:212)

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