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- PDB-6ezy: ARABIDOPSIS THALIANA GSTF9, GSH AND GSOH BOUND -

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Basic information

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


salicylic acid binding / toxin catabolic process / thylakoid / glutathione binding / plasmodesma / plant-type vacuole / apoplast / glutathione peroxidase activity / chloroplast stroma / response to zinc ion ...salicylic acid binding / toxin catabolic process / thylakoid / glutathione binding / plasmodesma / plant-type vacuole / apoplast / glutathione peroxidase activity / chloroplast stroma / response to zinc ion / glutathione transferase / glutathione transferase activity / response to cadmium ion / glutathione metabolic process / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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 / 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
BROMIDE ION / S-Hydroxy-Glutathione / GLUTATHIONE / Glutathione S-transferase F9
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsTossounian, M.A. / Wahni, K. / VanMolle, I. / Rosado, L. / Vertommen, D. / Messens, J.
Funding support Belgium, 5items
OrganizationGrant numberCountry
FWO Belgium
VIB-Marie Curie Cofund Belgium
VUBSRP34 Belgium
FWOG0D7914N 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 16, 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 1.2Jan 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 S-transferase F9
B: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2387
Polymers48,3562
Non-polymers8835
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-22 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.125, 114.125, 89.810
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 / 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 / Plasmid: PDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: O80852, glutathione transferase

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Non-polymers , 5 types, 221 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


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


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#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 / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.34 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: 0.10M 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: 2.34→49.418 Å / Num. obs: 28880 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 9.9 % / Biso Wilson estimate: 35.81 Å2 / Net I/σ(I): 18.3
Reflection shellResolution: 2.34→2.48 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 1.64 / % possible all: 96.8

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Processing

Software
NameClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RI6

4ri6


Resolution: 2.35→49.418 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.12
RfactorNum. reflection% reflection
Rfree0.1966 1368 4.8 %
Rwork0.1563 --
obs0.1583 28296 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.01 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 49 216 3565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123454
X-RAY DIFFRACTIONf_angle_d1.2674706
X-RAY DIFFRACTIONf_dihedral_angle_d13.1771239
X-RAY DIFFRACTIONf_chiral_restr0.051523
X-RAY DIFFRACTIONf_plane_restr0.007598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3502-2.43420.27741320.20732647X-RAY DIFFRACTION98
2.4342-2.53160.24021390.20462645X-RAY DIFFRACTION99
2.5316-2.64680.24321240.19352657X-RAY DIFFRACTION99
2.6468-2.78640.26461330.18222688X-RAY DIFFRACTION99
2.7864-2.96090.25641320.17972639X-RAY DIFFRACTION99
2.9609-3.18950.20231420.17782691X-RAY DIFFRACTION99
3.1895-3.51040.21771310.15782687X-RAY DIFFRACTION99
3.5104-4.01820.16751260.14212731X-RAY DIFFRACTION100
4.0182-5.06170.1471490.11642719X-RAY DIFFRACTION100
5.0617-49.42850.17991600.14942824X-RAY DIFFRACTION100
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)
11.42340.3279-0.55831.1438-0.14943.7443-0.1083-0.0067-0.082-0.04360.1321-0.03030.32170.1267-0.01590.2885-0.0716-0.03910.25180.02220.2744-40.214739.2871-11.5577
21.79350.35490.42661.17320.2182.7572-0.0679-0.02180.3011-0.15050.104-0.0067-0.4504-0.0003-0.03490.3076-0.0519-0.0310.23310.00580.3369-42.450361.3249-4.9007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 2:212)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 2:212)

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