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- PDB-9s3a: TaGST-10 in complex with deoxynivalenol-13-glutathione -

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Basic information

Entry
Database: PDB / ID: 9s3a
TitleTaGST-10 in complex with deoxynivalenol-13-glutathione
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GLUTATHIONE / DEOXYNIVALENOL / DETOXIFICATION / WHEAT / FUSARIUM
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / 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, N-terminal domain / Glutathione transferase family / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
: / : / ACETATE ION / Glutathione S-transferase
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMichlmayr, H. / Papageorgiou, A.C.
Funding support Austria, European Union, 3items
OrganizationGrant numberCountry
Austrian Science FundJ-4598 Austria
Austrian Science FundF3702,F3708,F3715 Austria
iNEXT-Discovery871037European Union
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Detoxification of deoxynivalenol by pathogen-inducible tau-class glutathione transferases from wheat.
Authors: Michlmayr, H. / Siller, M. / Kenjeric, L. / Doppler, M. / Malachova, A. / Hofer, M. / Hametner, C. / Schweiger, W. / Steiner, B. / Kugler, K.G. / Mayer, K.F.X. / Buerstmayr, H. / ...Authors: Michlmayr, H. / Siller, M. / Kenjeric, L. / Doppler, M. / Malachova, A. / Hofer, M. / Hametner, C. / Schweiger, W. / Steiner, B. / Kugler, K.G. / Mayer, K.F.X. / Buerstmayr, H. / Schuhmacher, R. / Krska, R. / Labrou, N.E. / Papageorgiou, A.C. / Adam, G.
History
DepositionJul 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,21519
Polymers49,8932
Non-polymers2,32217
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass photometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-90 kcal/mol
Surface area18690 Å2
Unit cell
Length a, b, c (Å)52.408, 61.859, 168.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11B-627-

HOH

21B-674-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione S-transferase


Mass: 24946.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: LOC123049460 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: A0A3B5XZG4, glutathione transferase

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Non-polymers , 7 types, 334 molecules

#2: Chemical ChemComp-A1I4U / Deoxynivalenol-13-glutathione


Mass: 603.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H37N3O12S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1I4T / Deoxynivalenol-13-cysteine


Mass: 417.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27NO8S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: needles
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→49.9 Å / Num. obs: 25016 / % possible obs: 99.3 % / Redundancy: 12.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.053 / Rrim(I) all: 0.19 / Χ2: 1.02 / Net I/σ(I): 10.5 / Num. measured all: 302782
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 98.7 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.978 / Num. measured all: 27411 / Num. unique obs: 2407 / CC1/2: 0.935 / Rpim(I) all: 0.287 / Rrim(I) all: 1.021 / Χ2: 0.97 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PHENIX1.20.1_4487model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.9 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.506 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25762 1280 5.1 %RANDOM
Rwork0.20997 ---
obs0.21248 23653 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0 Å2-0 Å2
2---0.46 Å20 Å2
3---1.41 Å2
Refinement stepCycle: 1 / Resolution: 2.3→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 152 317 3600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123344
X-RAY DIFFRACTIONr_bond_other_d0.0040.0163190
X-RAY DIFFRACTIONr_angle_refined_deg2.2811.844565
X-RAY DIFFRACTIONr_angle_other_deg1.031.7417390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.303512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15910524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023760
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02652
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6771.4261677
X-RAY DIFFRACTIONr_mcbond_other1.5691.4141672
X-RAY DIFFRACTIONr_mcangle_it2.5352.5392083
X-RAY DIFFRACTIONr_mcangle_other2.5352.542084
X-RAY DIFFRACTIONr_scbond_it1.9171.5981667
X-RAY DIFFRACTIONr_scbond_other1.9181.61668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2052.8412483
X-RAY DIFFRACTIONr_long_range_B_refined16.14217.663859
X-RAY DIFFRACTIONr_long_range_B_other15.45715.923744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 82 -
Rwork0.225 1696 -
obs--98.5 %
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)
11.4715-0.4649-0.54722.27110.00571.941-0.0318-0.06220.15480.10260.043-0.0625-0.09130.0972-0.01130.0104-0.0019-0.02010.0062-0.00480.526111.1943-14.3988-37.5777
22.144-0.7748-0.832.04780.30212.6794-0.0098-0.36750.03940.31680.005-0.0824-0.03830.15160.00480.06270.0016-0.00380.18020.030.450811.8341-28.8801-16.1687
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 503
2X-RAY DIFFRACTION2B7 - 501

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