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- PDB-7odm: AmGSTF1 Y118S variant -

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Basic information

Entry
Database: PDB / ID: 7odm
TitleAmGSTF1 Y118S variant
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione / glutathione-S-transferase
Function / homology
Function and homology information


response to chemical / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / 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 / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Chem-VDW / glutathione transferase
Similarity search - Component
Biological speciesAlopecurus myosuroides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPohl, E. / Eno, R.F.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/G006474/2 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
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1942
Polymers24,8861
Non-polymers3081
Water46826
1
AAA: Glutathione transferase
hetero molecules

AAA: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3884
Polymers49,7712
Non-polymers6172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+1/2,y,-z-1/41
Buried area2820 Å2
ΔGint-23 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.611, 112.611, 103.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Glutathione transferase


Mass: 24885.621 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: Chemical ChemComp-VDW / [(2~{S})-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]azanium


Mass: 308.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Morpheus screen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.6→45.34 Å / Num. obs: 10574 / % possible obs: 100 % / Redundancy: 26.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 22.7
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 1.01 / Num. unique obs: 1275

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TK8

6tk8


Resolution: 2.6→45.338 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.923 / SU B: 25.83 / SU ML: 0.251 / Cross valid method: FREE R-VALUE / ESU R: 0.376 / ESU R Free: 0.284
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.257 549 5.196 %
Rwork0.1878 10016 -
all0.191 --
obs-10565 99.962 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 76.103 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å20 Å20 Å2
2---2.43 Å2-0 Å2
3---4.861 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 20 26 1743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131763
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171631
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.642402
X-RAY DIFFRACTIONr_angle_other_deg1.3931.5753759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9495214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81122.38688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.60215275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.82158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_nbd_refined0.2230.2406
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21564
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2822
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.249
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1340.27
X-RAY DIFFRACTIONr_nbd_other0.1270.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3080.21
X-RAY DIFFRACTIONr_mcbond_it2.373.403859
X-RAY DIFFRACTIONr_mcbond_other2.3693.4858
X-RAY DIFFRACTIONr_mcangle_it3.715.0991072
X-RAY DIFFRACTIONr_mcangle_other3.7085.1021073
X-RAY DIFFRACTIONr_scbond_it2.7233.576904
X-RAY DIFFRACTIONr_scbond_other2.6773.572903
X-RAY DIFFRACTIONr_scangle_it4.1465.2851330
X-RAY DIFFRACTIONr_scangle_other4.1455.2881331
X-RAY DIFFRACTIONr_lrange_it7.64763.2817309
X-RAY DIFFRACTIONr_lrange_other7.63663.2267302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.397370.277725X-RAY DIFFRACTION99.8689
2.667-2.740.378310.287718X-RAY DIFFRACTION100
2.74-2.820.377340.287685X-RAY DIFFRACTION100
2.82-2.9060.255410.258667X-RAY DIFFRACTION100
2.906-3.0020.313360.283648X-RAY DIFFRACTION100
3.002-3.1070.395310.249633X-RAY DIFFRACTION100
3.107-3.2240.371350.244603X-RAY DIFFRACTION100
3.224-3.3550.295310.233591X-RAY DIFFRACTION100
3.355-3.5040.287340.236559X-RAY DIFFRACTION100
3.504-3.6750.351360.211536X-RAY DIFFRACTION100
3.675-3.8730.227310.2522X-RAY DIFFRACTION100
3.873-4.1070.299140.169490X-RAY DIFFRACTION100
4.107-4.390.185320.154459X-RAY DIFFRACTION100
4.39-4.7410.164300.129432X-RAY DIFFRACTION100
4.741-5.1910.235290.133391X-RAY DIFFRACTION100
5.191-5.8010.321110.15376X-RAY DIFFRACTION100
5.801-6.6930.149260.143321X-RAY DIFFRACTION100
6.693-8.1820.14140.155283X-RAY DIFFRACTION100
8.182-11.5110.18120.138238X-RAY DIFFRACTION100
11.511-45.3380.389140.239139X-RAY DIFFRACTION98.7097
Refinement TLS params.Method: refined / Origin x: 21.1517 Å / Origin y: 1.6452 Å / Origin z: -22.6193 Å
111213212223313233
T0.4532 Å20.0272 Å20.219 Å2-0.3787 Å2-0.3035 Å2--0.4538 Å2
L4.7439 °20.8305 °2-2.0561 °2-0.4419 °2-0.3676 °2--4.2606 °2
S-0.4298 Å °0.2882 Å °-0.0609 Å °-0.2127 Å °-0.2514 Å °0.1403 Å °0.1411 Å °-0.487 Å °0.6812 Å °
Refinement TLS groupSelection: ALL

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