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- PDB-6f05: ARABIDOPSIS THALIANA GSTF9, GSO3 BOUND -

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Basic information

Entry
Database: PDB / ID: 6f05
TitleARABIDOPSIS THALIANA GSTF9, GSO3 BOUND
ComponentsGlutathione S-transferase F9
KeywordsTRANSFERASE / PHI CLASS / PEROXIDASE / GSO3
Function / homology
Function and homology information


salicylic acid binding / toxin catabolic process / glutathione binding / thylakoid / apoplast / plasmodesma / plant-type vacuole / glutathione peroxidase activity / chloroplast stroma / response to zinc ion ...salicylic acid binding / toxin catabolic process / glutathione binding / thylakoid / apoplast / plasmodesma / plant-type vacuole / 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, C-terminal / 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. / 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, C-terminal / 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. / 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 SULFONIC ACID / Glutathione S-transferase F9
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTossounian, M.A. / Wahni, K. / VanMolle, I. / Vertommen, D. / Rosado, L. / 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 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 1.2Jan 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
C: Glutathione S-transferase F9
D: Glutathione S-transferase F9
E: Glutathione S-transferase F9
F: Glutathione S-transferase F9
G: Glutathione S-transferase F9
H: Glutathione S-transferase F9
I: Glutathione S-transferase F9
J: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,01933
Polymers241,77910
Non-polymers4,24123
Water13,241735
1
I: Glutathione S-transferase F9
hetero molecules

C: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1376
Polymers48,3562
Non-polymers7824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
2
A: Glutathione S-transferase F9
B: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,50610
Polymers48,3562
Non-polymers1,1508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-45 kcal/mol
Surface area16150 Å2
MethodPISA
3
C: Glutathione S-transferase F9
hetero molecules

I: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1376
Polymers48,3562
Non-polymers7824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4220 Å2
ΔGint-42 kcal/mol
Surface area16020 Å2
MethodPISA
4
D: Glutathione S-transferase F9
E: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1376
Polymers48,3562
Non-polymers7824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-41 kcal/mol
Surface area15280 Å2
MethodPISA
5
F: Glutathione S-transferase F9
J: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1025
Polymers48,3562
Non-polymers7463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-28 kcal/mol
Surface area15120 Å2
MethodPISA
6
G: Glutathione S-transferase F9
H: Glutathione S-transferase F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1376
Polymers48,3562
Non-polymers7824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-39 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.430, 93.970, 107.710
Angle α, β, γ (deg.)93.19, 101.57, 101.97
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 24177.865 Da / Num. of mol.: 10
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 (E. coli) / References: UniProt: O80852, glutathione transferase
#2: Chemical
ChemComp-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C10H17N3O9S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: 0.1 M LiCl, 0.1 M Tris-HCl pH 8.0 and 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→65.731 Å / Num. obs: 116579 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Biso Wilson estimate: 33.79 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.67
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.08 / % possible all: 97.1

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Processing

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

6ezy


Resolution: 2.2→65.731 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.27
RfactorNum. reflection% reflection
Rfree0.2093 5642 4.95 %
Rwork0.1615 --
obs0.1638 114041 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→65.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15509 0 263 735 16507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816193
X-RAY DIFFRACTIONf_angle_d1.1822113
X-RAY DIFFRACTIONf_dihedral_angle_d12.1095672
X-RAY DIFFRACTIONf_chiral_restr0.0472480
X-RAY DIFFRACTIONf_plane_restr0.0072809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.28571850.23323519X-RAY DIFFRACTION97
2.225-2.25120.28772130.23233555X-RAY DIFFRACTION97
2.2512-2.27860.28621870.22783604X-RAY DIFFRACTION97
2.2786-2.30750.29741870.22533542X-RAY DIFFRACTION97
2.3075-2.33780.25981720.20663606X-RAY DIFFRACTION98
2.3378-2.36990.2461710.19863647X-RAY DIFFRACTION98
2.3699-2.40370.25861960.18913597X-RAY DIFFRACTION97
2.4037-2.43960.24881920.18743619X-RAY DIFFRACTION98
2.4396-2.47770.25061870.19173612X-RAY DIFFRACTION98
2.4777-2.51840.24251760.1873603X-RAY DIFFRACTION98
2.5184-2.56180.25441770.18393635X-RAY DIFFRACTION97
2.5618-2.60840.24911770.18153610X-RAY DIFFRACTION98
2.6084-2.65850.26232050.17543589X-RAY DIFFRACTION98
2.6585-2.71280.25231920.17953578X-RAY DIFFRACTION98
2.7128-2.77180.241970.17323635X-RAY DIFFRACTION98
2.7718-2.83630.24941900.17193588X-RAY DIFFRACTION98
2.8363-2.90720.2192030.16943624X-RAY DIFFRACTION98
2.9072-2.98580.22631780.16743659X-RAY DIFFRACTION98
2.9858-3.07370.23212060.1733618X-RAY DIFFRACTION98
3.0737-3.17290.22331840.17523600X-RAY DIFFRACTION98
3.1729-3.28630.21691940.16783615X-RAY DIFFRACTION98
3.2863-3.41780.1981830.16273691X-RAY DIFFRACTION99
3.4178-3.57340.18571800.1473621X-RAY DIFFRACTION99
3.5734-3.76180.20211910.14843654X-RAY DIFFRACTION98
3.7618-3.99740.16881880.14143631X-RAY DIFFRACTION99
3.9974-4.3060.16562110.12223641X-RAY DIFFRACTION98
4.306-4.73920.15521840.12453647X-RAY DIFFRACTION99
4.7392-5.42470.18561860.13943614X-RAY DIFFRACTION98
5.4247-6.83340.20671750.16143662X-RAY DIFFRACTION98
6.8334-65.76080.1811750.15643583X-RAY DIFFRACTION97
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)
11.5819-0.1577-0.27440.88750.11441.02260.01950.1572-0.203-0.1435-0.036-0.04090.0519-0.03060.01520.2411-0.0180.02570.1978-0.03410.3326-53.4696-14.2592-46.4445
22.3789-0.4095-0.01281.1871-0.02790.8390.00950.1360.1912-0.15320.0167-0.084-0.12090.0141-0.0190.235-0.02850.02460.1513-0.00310.2767-60.57946.4007-38.6839
31.4665-0.2766-0.09412.06760.06621.8863-0.0401-0.17460.04120.33840.01640.0794-0.02370.030.02150.2817-0.03970.01020.16950.01920.3232-31.5444-30.8295-25.4208
41.7756-0.7961-0.86382.06810.20783.0231-0.0757-0.89840.32210.34410.3357-0.0325-0.13620.482-0.16320.32270.0076-0.00220.6841-0.16510.309-19.544421.44212.8378
52.9203-0.632-0.38671.90540.48272.5014-0.1851-0.514-0.28360.33350.16650.15470.2950.0648-0.01290.25720.01250.01940.29960.04640.2087-21.04434.0262-11.8282
62.0055-0.8912-1.03882.73980.25912.11220.18650.2334-0.3162-0.3497-0.37810.3487-0.0660.00180.18180.33760.0858-0.01190.4387-0.11990.3695-29.4544-28.1259-76.5371
71.84190.17920.161.5863-0.42370.7690.19660.1996-0.1463-0.4286-0.21050.03760.46020.31860.03190.56520.12790.06390.5786-0.00660.3024-30.845726.6458-72.8266
81.7992-1.12151.20062.5412-0.9281.32420.20890.15170.13130.0468-0.3216-0.39780.10520.28250.09720.34090.00730.04320.61390.02730.3379-20.46141.3409-58.6891
91.1375-0.3290.49012.4606-0.02191.1670.0288-0.1121-0.2620.24230.04770.31530.1293-0.0342-0.07720.282-0.04860.02170.18880.05350.3874-51.455738.3525-26.4644
101.6712-0.1273-0.15411.4264-0.1562.45080.15380.7192-0.1668-0.7362-0.4030.66-0.2956-0.35850.26340.88870.3057-0.31210.7633-0.28760.6091-41.9313-21.1255-94.2295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:213)
2X-RAY DIFFRACTION2(chain B and resseq 2:215)
3X-RAY DIFFRACTION3(chain C and resseq 2:213)
4X-RAY DIFFRACTION4(chain D and resseq 3:213)
5X-RAY DIFFRACTION5(chain E and resseq 2:213)
6X-RAY DIFFRACTION6(chain F and resseq 2:213)
7X-RAY DIFFRACTION7(chain G and resseq 3:212)
8X-RAY DIFFRACTION8(chain H and resseq 2:213)
9X-RAY DIFFRACTION9(chain I and resseq 2:213)
10X-RAY DIFFRACTION10(chain J and resseq 2:212)

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