PDB-6tk8: GSTF1 F122T variant from Alopecurus myosuroides

ID or keywords:

Entry

Database: PDB / ID: 6tk8

Title

GSTF1 F122T variant from Alopecurus myosuroides

Components

Glutathione transferase

Keywords

TRANSFERASE / 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

Biological species

Alopecurus myosuroides (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.78 Å

Authors

Pohl, E. / Eno, R.F.M. / Freitag-Pohl, S. / Steel, P.G.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: GSTF1 from Alopecurus myosuroides
Authors: Pohl, E. / Eno, R.F.M. / Freitag-Pohl, S. / Steel, P.G.

History

Deposition	Nov 28, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 26, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6tk8.cif.gz	89.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6tk8.ent.gz		Display	PDB format
PDBx/mmJSON format	6tk8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6tk8_validation.pdf.gz	673.3 KB	Display	wwPDB validaton report
Full document	6tk8_full_validation.pdf.gz	675.7 KB	Display
Data in XML	6tk8_validation.xml.gz	10.2 KB	Display
Data in CIF	6tk8_validation.cif.gz	13 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tk/6tk8 ftp://data.pdbj.org/pub/pdb/validation_reports/tk/6tk8	HTTPS FTP

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Related structure data

Related structure data	6tjsSC 6tnlC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4pnf-2 6f01-d 4jed-1 4ri7-d 3vwx-1 5f06-d 3lkj-d 2vd0-2 6ezy-d 4pnf-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (9) #255 - Mar 2021 Cisplatin and DNA similarity (8)

Deposited unit

AAA: Glutathione transferase

hetero molecules

25.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Glutathione transferase

hetero molecules

AAA: Glutathione transferase

hetero molecules

defined by author&software
Evidence: gel filtration
50.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	112.590, 112.590, 104.300
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22

#1: Protein	Glutathione transferase Mass: 24915.648 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.: 5 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.32 Å³/Da / Density % sol: 62.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Morpheus screen

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 2.78→43.6 Å / Num. obs: 8791 / % possible obs: 99.8 % / Redundancy: 1.8 % / R_merge(I) obs: 0.04 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.78→2.93 Å / R_merge(I) obs: 0.456 / Num. unique obs: 315 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
DIALS		data reduction
DIALS		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6TJS

6tjs

Resolution: 2.78→43.6 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.938 / Cross valid method: FREE R-VALUE / ESU R: 0.532 / ESU R Free: 0.32
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2505	478	5.484 %
R_work	0.1802	-	-
all	0.184	-	-
obs	-	8717	99.725 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 78.244 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.003 Å²	0 Å²	0 Å²
2-	-	-3.003 Å²	0 Å²
3-	-	-	6.005 Å²

Refinement step

Cycle: LAST / Resolution: 2.78→43.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1649	0	20	5	1674

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	1714
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.017	1568
X-RAY DIFFRACTION	r_angle_refined_deg	1.679	1.637	2340
X-RAY DIFFRACTION	r_angle_other_deg	2.402	1.566	3613
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.81	5	212
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.086	21.728	81
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.486	15	252
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.996	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	225
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1925
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	371
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	426
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.233	0.2	1467
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	791
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.096	0.2	759
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	38
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.128	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.257	0.2	46
X-RAY DIFFRACTION	r_mcbond_it	7.507	8.259	851
X-RAY DIFFRACTION	r_mcbond_other	7.508	8.255	850
X-RAY DIFFRACTION	r_mcangle_it	10.815	12.389	1062
X-RAY DIFFRACTION	r_mcangle_other	10.81	12.395	1063
X-RAY DIFFRACTION	r_scbond_it	7.978	8.704	863
X-RAY DIFFRACTION	r_scbond_other	7.981	8.7	862
X-RAY DIFFRACTION	r_scangle_it	11.93	12.809	1278
X-RAY DIFFRACTION	r_scangle_other	11.925	12.811	1279
X-RAY DIFFRACTION	r_lrange_it	14.497	97.363	1910
X-RAY DIFFRACTION	r_lrange_other	14.498	97.363	1911

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.78-2.852	0.412	32	0.349	600	X-RAY DIFFRACTION	99.842
2.852-2.93	0.386	35	0.323	570	X-RAY DIFFRACTION	100
2.93-3.015	0.299	26	0.297	576	X-RAY DIFFRACTION	100
3.015-3.108	0.367	27	0.266	560	X-RAY DIFFRACTION	99.8299
3.108-3.209	0.369	25	0.254	532	X-RAY DIFFRACTION	100
3.209-3.322	0.315	33	0.242	522	X-RAY DIFFRACTION	100
3.322-3.447	0.246	36	0.223	480	X-RAY DIFFRACTION	99.0403
3.447-3.587	0.298	25	0.194	500	X-RAY DIFFRACTION	100
3.587-3.747	0.249	30	0.167	454	X-RAY DIFFRACTION	99.7938
3.747-3.929	0.208	36	0.151	432	X-RAY DIFFRACTION	99.5745
3.929-4.141	0.236	22	0.123	436	X-RAY DIFFRACTION	99.7821
4.141-4.391	0.191	18	0.132	405	X-RAY DIFFRACTION	99.7642
4.391-4.694	0.271	27	0.128	368	X-RAY DIFFRACTION	99.2462
4.694-5.068	0.214	40	0.128	340	X-RAY DIFFRACTION	100
5.068-5.55	0.222	17	0.151	332	X-RAY DIFFRACTION	99.7143
5.55-6.201	0.243	6	0.172	316	X-RAY DIFFRACTION	100
6.201-7.153	0.324	9	0.231	278	X-RAY DIFFRACTION	100
7.153-8.743	0.28	15	0.166	240	X-RAY DIFFRACTION	100
8.743-12.29	0.147	12	0.157	180	X-RAY DIFFRACTION	100
12.29-43.6	0.301	7	0.231	118	X-RAY DIFFRACTION	96.1538

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