PDB-6tjs: GSTF1 from Alopecurus myosuroides

ID or keywords:

Entry

Database: PDB / ID: 6tjs

Title

GSTF1 from Alopecurus myosuroides

Components

Glutathione transferase

Keywords

TRANSFERASE / 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 / cytoplasm
Similarity search - Function

Biological species

Alopecurus myosuroides (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.53 Å

Authors

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

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.

History

Deposition	Nov 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 12, 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: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6tjs.cif.gz	86.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6tjs.ent.gz		Display	PDB format
PDBx/mmJSON format	6tjs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6tjs_validation.pdf.gz	428.2 KB	Display	wwPDB validaton report
Full document	6tjs_full_validation.pdf.gz	429.4 KB	Display
Data in XML	6tjs_validation.xml.gz	10.2 KB	Display
Data in CIF	6tjs_validation.cif.gz	14 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/6tjs ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tjs	HTTPS FTP

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Related structure data

Related structure data	6tk8C 6tnlC 1axdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1s9v-2 6kvm-d 3c5j-d 1s9v-1 6bix-d 4m5t-d 2q6w-1 3fxj-d 3ffb-d 4n0e-d 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

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

1

AAA: Glutathione transferase

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

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 number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	AAA-333- HOH
2	1	AAA-335- HOH

#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 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: 2.45 Å³/Da / Density % sol: 49.71 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.916 Å / Relative weight: 1
Reflection	Resolution: 1.53→52 Å / Num. obs: 38156 / % possible obs: 100 % / Redundancy: 12.6 % / R_merge(I) obs: 0.034 / R_pim(I) all: 0.014 / Net I/σ(I): 27.3
Reflection shell	Resolution: 1.53→1.6 Å / R_merge(I) obs: 0.079 / Num. unique obs: 1848

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1AXD

1axd

Resolution: 1.53→51.847 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.2058	1886	4.951 %
R_work	0.1928	-	-
all	0.193	-	-
obs	-	38090	99.851 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.173 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.238 Å²	0.119 Å²	0 Å²
2-	-	0.238 Å²	0 Å²
3-	-	-	-0.773 Å²

Refinement step

Cycle: LAST / Resolution: 1.53→51.847 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1522	0	0	112	1634

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	1582
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	1464
X-RAY DIFFRACTION	r_angle_refined_deg	1.818	1.638	2163
X-RAY DIFFRACTION	r_angle_other_deg	2.304	1.568	3385
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.068	5	195
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.613	22.468	77
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.321	15	242
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.103	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	203
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	1765
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	344
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	322
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.222	0.2	1231
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	786
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	654
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	75
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.188	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.072	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	3.007	2.972	771
X-RAY DIFFRACTION	r_mcbond_other	3.006	2.967	770
X-RAY DIFFRACTION	r_mcangle_it	4.339	4.421	960
X-RAY DIFFRACTION	r_mcangle_other	4.337	4.427	961
X-RAY DIFFRACTION	r_scbond_it	4.181	3.324	810
X-RAY DIFFRACTION	r_scbond_other	4.171	3.324	810
X-RAY DIFFRACTION	r_scangle_it	6.129	4.866	1199
X-RAY DIFFRACTION	r_scangle_other	6.13	4.861	1198
X-RAY DIFFRACTION	r_lrange_it	7.51	35.264	1798
X-RAY DIFFRACTION	r_lrange_other	7.514	35.032	1782

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.53-1.57	0.327	136	0.312	2625	0.313	2774	0.832	0.83	99.5314	0.3
1.57-1.613	0.308	106	0.287	2581	0.288	2692	0.836	0.852	99.8143	0.271
1.613-1.659	0.288	134	0.263	2464	0.264	2606	0.881	0.888	99.693	0.24
1.659-1.71	0.278	133	0.241	2425	0.242	2560	0.878	0.901	99.9219	0.216
1.71-1.767	0.278	121	0.224	2354	0.227	2478	0.897	0.919	99.8789	0.196
1.767-1.828	0.261	112	0.219	2289	0.221	2407	0.906	0.927	99.7507	0.187
1.828-1.897	0.214	128	0.21	2180	0.21	2312	0.938	0.937	99.827	0.181
1.897-1.975	0.237	107	0.204	2142	0.205	2250	0.93	0.945	99.9556	0.179
1.975-2.062	0.224	114	0.194	2029	0.195	2146	0.942	0.952	99.8602	0.174
2.062-2.163	0.208	117	0.191	1941	0.192	2059	0.948	0.951	99.9514	0.173
2.163-2.28	0.218	83	0.174	1879	0.176	1965	0.948	0.962	99.8473	0.159
2.28-2.418	0.185	98	0.175	1782	0.175	1881	0.957	0.96	99.9468	0.163
2.418-2.584	0.2	92	0.171	1658	0.173	1750	0.947	0.963	100	0.163
2.584-2.791	0.224	80	0.177	1565	0.179	1647	0.945	0.96	99.8786	0.173
2.791-3.056	0.173	61	0.185	1464	0.185	1526	0.961	0.96	99.9345	0.185
3.056-3.415	0.219	72	0.204	1321	0.205	1394	0.941	0.953	99.9283	0.212
3.415-3.941	0.19	70	0.178	1174	0.178	1244	0.964	0.965	100	0.194
3.941-4.82	0.168	50	0.167	1016	0.167	1066	0.971	0.967	100	0.193
4.82-6.787	0.19	35	0.193	818	0.193	854	0.969	0.968	99.8829	0.227
6.787-51.847	0.2	37	0.22	496	0.218	533	0.963	0.949	100	0.257

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