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- PDB-6to3: GSTF1 from Alopecurus myosuroides - covalently modified -

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Basic information

Entry
Database: PDB / ID: 6to3
TitleGSTF1 from Alopecurus myosuroides - covalently modified
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione-S-transferase / Ligandin / flavonoid binding / mult-herbicide resistence
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
4-chloro-7-nitrobenzofurazan / glutathione transferase
Similarity search - Component
Biological speciesAlopecurus myosuroides (plant)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.798 Å
AuthorsPohl, E. / Eno, R.F.M. / Freitag-Pohl, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/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
DepositionDec 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 2.0Aug 31, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / citation / citation_author / entity / entity_src_gen / pdbx_entity_nonpoly / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.pdbx_synonyms / _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 / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag

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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)35,0542
Polymers34,8541
Non-polymers2001
Water1448
1
AAA: Glutathione transferase
hetero molecules

AAA: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1084
Polymers69,7092
Non-polymers3992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area2690 Å2
ΔGint-20 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.760, 104.760, 79.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Glutathione transferase


Mass: 34854.270 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-5Z8 / 4-chloro-7-nitrobenzofurazan / 4-chloranyl-7-nitro-2,1,3-benzoxadiazole / NBD-Cl / 4-nitro-2,1,3-benzoxadiazole (post-reaction)


Mass: 199.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H2ClN3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 1.83 Å3/Da / Density % sol: 32.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: Na/K tartrate and ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jun 1, 2011
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.798→59.808 Å / Num. obs: 6748 / % possible obs: 100 % / Redundancy: 50.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.3
Reflection shellResolution: 2.798→2.86 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 357 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.798→59.808 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: FREE R-VALUE / ESU R: 1.208 / ESU R Free: 0.389
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2808 316 4.735 %
Rwork0.2081 --
all0.211 --
obs-6674 99.035 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.904 Å2
Baniso -1Baniso -2Baniso -3
1--0.045 Å2-0.023 Å20 Å2
2---0.045 Å20 Å2
3---0.146 Å2
Refinement stepCycle: LAST / Resolution: 2.798→59.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 18 8 1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131536
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171403
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.652099
X-RAY DIFFRACTIONr_angle_other_deg2.3831.573221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22522.08372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92115216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.41157
X-RAY DIFFRACTIONr_chiral_restr0.0710.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021706
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02334
X-RAY DIFFRACTIONr_nbd_refined0.2260.2374
X-RAY DIFFRACTIONr_symmetry_nbd_other0.230.21244
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2739
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.229
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3760.26
X-RAY DIFFRACTIONr_nbd_other0.220.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2310.21
X-RAY DIFFRACTIONr_mcbond_it3.1544.035759
X-RAY DIFFRACTIONr_mcbond_other3.1244.03758
X-RAY DIFFRACTIONr_mcangle_it4.7376.013938
X-RAY DIFFRACTIONr_mcangle_other4.7356.02939
X-RAY DIFFRACTIONr_scbond_it3.4664.409776
X-RAY DIFFRACTIONr_scbond_other3.4644.413777
X-RAY DIFFRACTIONr_scangle_it5.3486.51160
X-RAY DIFFRACTIONr_scangle_other5.3466.5051161
X-RAY DIFFRACTIONr_lrange_it7.72647.5941743
X-RAY DIFFRACTIONr_lrange_other7.72947.591743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.798-2.8710.365290.293437X-RAY DIFFRACTION99.3603
2.871-2.950.373290.295442X-RAY DIFFRACTION99.3671
2.95-3.0350.535180.26431X-RAY DIFFRACTION99.5565
3.035-3.1280.284250.251423X-RAY DIFFRACTION99.5556
3.128-3.2310.27260.232402X-RAY DIFFRACTION99.7669
3.231-3.3440.304200.217397X-RAY DIFFRACTION98.5816
3.344-3.470.235160.228398X-RAY DIFFRACTION99.759
3.47-3.6110.182120.203371X-RAY DIFFRACTION98.9664
3.611-3.7720.336160.191363X-RAY DIFFRACTION98.6979
3.772-3.9560.217200.191335X-RAY DIFFRACTION98.8858
3.956-4.1690.248150.193327X-RAY DIFFRACTION98.5591
4.169-4.4210.2690.188315X-RAY DIFFRACTION99.0826
4.421-4.7260.292140.187296X-RAY DIFFRACTION98.4127
4.726-5.1030.22450.181281X-RAY DIFFRACTION98.9619
5.103-5.5890.335160.2258X-RAY DIFFRACTION98.5611
5.589-6.2450.184120.185233X-RAY DIFFRACTION98.7903
6.245-7.2060.394100.193214X-RAY DIFFRACTION98.2456
7.206-8.8110.22570.133189X-RAY DIFFRACTION98.9899
8.811-12.4030.235150.153143X-RAY DIFFRACTION100
12.403-59.8080.17220.39103X-RAY DIFFRACTION96.3303

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