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- PDB-6tjs: GSTF1 from Alopecurus myosuroides -

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Basic information

Entry
Database: PDB / ID: 6tjs
TitleGSTF1 from Alopecurus myosuroides
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione-S-transferase / Ligandin / flavonoid binding / mult-herbicide resistence
Function / homology
Function and homology information


glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / response to toxic substance / cytoplasm
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / 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
glutathione transferase
Similarity search - Component
Biological speciesAlopecurus myosuroides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPohl, E. / Eno, R.F.M. / Freitag-Pohl, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/G006474/1 United Kingdom
CitationJournal: Org.Biomol.Chem. / Year: 2021
Title: Flavonoid-based inhibitors of the Phi-class glutathione transferase from black-grass to combat multiple herbicide resistance.
Authors: Schwarz, M. / Eno, R.F.M. / Freitag-Pohl, S. / Coxon, C.R. / Straker, H.E. / Wortley, D.J. / Hughes, D.J. / Mitchell, G. / Moore, J. / Cummins, I. / Onkokesung, N. / Brazier-Hicks, M. / ...Authors: Schwarz, M. / Eno, R.F.M. / Freitag-Pohl, S. / Coxon, C.R. / Straker, H.E. / Wortley, D.J. / Hughes, D.J. / Mitchell, G. / Moore, J. / Cummins, I. / Onkokesung, N. / Brazier-Hicks, M. / Edwards, R. / Pohl, E. / Steel, P.G.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glutathione transferase


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water2,018112
1
AAA: Glutathione transferase

AAA: Glutathione transferase


Theoretical massNumber of molelcules
Total (without water)49,9882
Polymers49,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area2750 Å2
ΔGint-25 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.695, 103.695, 78.769
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11AAA-333-

HOH

21AAA-335-

HOH

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Components

#1: Protein Glutathione transferase


Mass: 24993.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alopecurus myosuroides (plant) / Gene: GST2c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZS17, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 49.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate pH 5.6, Na/K tartrate 1.5-2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.53→52 Å / Num. obs: 38156 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.014 / Net I/σ(I): 27.3
Reflection shellResolution: 1.53→1.6 Å / Rmerge(I) obs: 0.079 / Num. unique obs: 1848

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXD

1axd


Resolution: 1.53→51.847 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2058 1886 4.951 %
Rwork0.1928 --
all0.193 --
obs-38090 99.851 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.173 Å2
Baniso -1Baniso -2Baniso -3
1-0.238 Å20.119 Å20 Å2
2--0.238 Å20 Å2
3----0.773 Å2
Refinement stepCycle: LAST / Resolution: 1.53→51.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 0 112 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131582
X-RAY DIFFRACTIONr_bond_other_d0.0340.0171464
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.6382163
X-RAY DIFFRACTIONr_angle_other_deg2.3041.5683385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0685195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.61322.46877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32115242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.103157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021765
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02344
X-RAY DIFFRACTIONr_nbd_refined0.2340.2322
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.21231
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2786
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.275
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.29
X-RAY DIFFRACTIONr_nbd_other0.1910.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0720.29
X-RAY DIFFRACTIONr_mcbond_it3.0072.972771
X-RAY DIFFRACTIONr_mcbond_other3.0062.967770
X-RAY DIFFRACTIONr_mcangle_it4.3394.421960
X-RAY DIFFRACTIONr_mcangle_other4.3374.427961
X-RAY DIFFRACTIONr_scbond_it4.1813.324810
X-RAY DIFFRACTIONr_scbond_other4.1713.324810
X-RAY DIFFRACTIONr_scangle_it6.1294.8661199
X-RAY DIFFRACTIONr_scangle_other6.134.8611198
X-RAY DIFFRACTIONr_lrange_it7.5135.2641798
X-RAY DIFFRACTIONr_lrange_other7.51435.0321782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.53-1.570.3271360.31226250.31327740.8320.8399.53140.3
1.57-1.6130.3081060.28725810.28826920.8360.85299.81430.271
1.613-1.6590.2881340.26324640.26426060.8810.88899.6930.24
1.659-1.710.2781330.24124250.24225600.8780.90199.92190.216
1.71-1.7670.2781210.22423540.22724780.8970.91999.87890.196
1.767-1.8280.2611120.21922890.22124070.9060.92799.75070.187
1.828-1.8970.2141280.2121800.2123120.9380.93799.8270.181
1.897-1.9750.2371070.20421420.20522500.930.94599.95560.179
1.975-2.0620.2241140.19420290.19521460.9420.95299.86020.174
2.062-2.1630.2081170.19119410.19220590.9480.95199.95140.173
2.163-2.280.218830.17418790.17619650.9480.96299.84730.159
2.28-2.4180.185980.17517820.17518810.9570.9699.94680.163
2.418-2.5840.2920.17116580.17317500.9470.9631000.163
2.584-2.7910.224800.17715650.17916470.9450.9699.87860.173
2.791-3.0560.173610.18514640.18515260.9610.9699.93450.185
3.056-3.4150.219720.20413210.20513940.9410.95399.92830.212
3.415-3.9410.19700.17811740.17812440.9640.9651000.194
3.941-4.820.168500.16710160.16710660.9710.9671000.193
4.82-6.7870.19350.1938180.1938540.9690.96899.88290.227
6.787-51.8470.2370.224960.2185330.9630.9491000.257

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