PDB-9ufc: Structural of a glutamate cysteine ligase StGSH1 in Solanum tuberosum

ID or keywords:

Entry

Database: PDB / ID: 9ufc

Title

Structural of a glutamate cysteine ligase StGSH1 in Solanum tuberosum

Components

Glutamate--cysteine ligase, chloroplastic

Keywords

PLANT PROTEIN / glutamate cysteine ligase / glutathione

Function / homology

Function and homology information

indole phytoalexin biosynthetic process / glucosinolate biosynthetic process / defense response by callose deposition in cell wall / glutamate-cysteine ligase / glutamate-cysteine ligase activity / defense response to insect / flower development / response to ozone / glutathione biosynthetic process / response to jasmonic acid ...
Similarity search - Function

Biological species

Solanum tuberosum (potato)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.53 Å

Authors

Zhao, H.B. / Fan, S.L.

Funding support

China, 1items

Citation

Journal: J. Biol. Chem. / Year: 2006
Title: Structural basis for the redox control of plant glutamate cysteine ligase
Authors: Hothorn, M. / Wachter, A.

History

Deposition	Apr 10, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 15, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ufc.cif.gz	704.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9ufc.ent.gz	586.4 KB	Display	PDB format
PDBx/mmJSON format	9ufc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uf/9ufc ftp://data.pdbj.org/pub/pdb/validation_reports/uf/9ufc	HTTPS FTP

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Related structure data

Related structure data	2gwcC 2gwdC C: citing same article (ref.)
Similar structure data	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	#30 - Jun 2002 Glutamine Synthetase similarity (1)

Deposited unit

A: Glutamate--cysteine ligase, chloroplastic

B: Glutamate--cysteine ligase, chloroplastic

C: Glutamate--cysteine ligase, chloroplastic

D: Glutamate--cysteine ligase, chloroplastic

236 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutamate--cysteine ligase, chloroplastic

C: Glutamate--cysteine ligase, chloroplastic

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

2

B: Glutamate--cysteine ligase, chloroplastic

D: Glutamate--cysteine ligase, chloroplastic

defined by author
118 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.652, 179.086, 193.223
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Glutamate--cysteine ligase, chloroplastic / Gamma-ECS / Gamma-glutamylcysteine synthetase Mass: 58943.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum tuberosum (potato) / Gene: LOC102600891 / Production host: Escherichia coli (E. coli) / References: UniProt: M1AWB9, glutamate-cysteine ligase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.18 Å³/Da / Density % sol: 43.49 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 22% PEG3350, 0.1M Bis-Tris pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: Y
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 2.53→46.69 Å / Num. obs: 67371 / % possible obs: 98.25 % / Redundancy: 5.6 % / R_rim(I) all: 0.119 / Net I/σ(I): 14.32
Reflection shell	Resolution: 2.53→2.62 Å / Num. unique obs: 67337 / R_rim(I) all: 0.119
Serial crystallography sample delivery	Method: fixed target

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.53→46.69 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2407	2000	2.97 %
R_work	0.1908	-	-
obs	0.1923	67337	98.27 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.53→46.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13928	0	0	182	14110

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	5.299	1914
X-RAY DIFFRACTION	f_chiral_restr	0.043	2031
X-RAY DIFFRACTION	f_plane_restr	0.006	2510

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 (%)
2.53-2.6	0.3337	139	0.2906	4572	X-RAY DIFFRACTION	97
2.6-2.67	0.301	142	0.2685	4635	X-RAY DIFFRACTION	98
2.67-2.75	0.3575	142	0.2623	4632	X-RAY DIFFRACTION	99
2.75-2.83	0.3101	144	0.2467	4685	X-RAY DIFFRACTION	99
2.83-2.94	0.2953	142	0.2362	4616	X-RAY DIFFRACTION	99
2.94-3.05	0.2982	142	0.2305	4669	X-RAY DIFFRACTION	99
3.05-3.19	0.3127	141	0.2299	4604	X-RAY DIFFRACTION	98
3.19-3.36	0.3074	140	0.2389	4578	X-RAY DIFFRACTION	97
3.36-3.57	0.2548	145	0.19	4713	X-RAY DIFFRACTION	100
3.57-3.85	0.2155	144	0.1846	4709	X-RAY DIFFRACTION	99
3.85-4.23	0.206	143	0.1626	4697	X-RAY DIFFRACTION	99
4.23-4.84	0.2007	141	0.1465	4617	X-RAY DIFFRACTION	97
4.84-6.1	0.2029	147	0.1708	4779	X-RAY DIFFRACTION	99
6.1-46.69	0.1898	148	0.1543	4831	X-RAY DIFFRACTION	97

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.8701	-0.0788	0.2546	0.5845	0.2266	1.3197	0.0706	-0.0438	-0.1485	0.0972	-0.091	-0.0498	0.1215	-0.0426	0.0262	0.3821	-0.1228	-0.0451	0.225	0.0782	0.4016	2.0426	19.2401	-25.3618
2	1.9173	-0.4263	-0.4847	0.5495	0.114	1.2223	0.1228	-0.2808	0.021	0.1154	-0.0604	-0.0382	0.042	-0.0028	-0.0426	0.4161	-0.1215	-0.0951	0.3233	0.0685	0.4232	12.646	25.9921	-17.3493
3	0.9995	0.0227	0.0381	0.744	0.5157	0.5896	-0.0151	-0.8473	-0.5459	0.27	0.0762	0.2046	0.4867	-0.4526	0.0854	0.7111	-0.2702	-0.0474	0.5895	0.2469	0.5783	-4.597	9.4305	-9.1449
4	1.1375	-0.1391	-0.1059	0.4055	-0.0688	0.735	0.1142	0.439	0.0408	-0.1002	-0.1247	0.025	0.2177	0.0217	0.0098	0.541	0.2285	0.0472	0.5568	0.0273	0.3892	-35.1727	32.5283	17.3426
5	1.0967	-0.1418	-0.2008	0.3121	-0.1928	0.4996	0.0453	0.417	0.0606	-0.0575	-0.0361	-0.1228	0.1587	-0.0458	0.0187	0.584	0.2148	0.0829	0.5683	-0.0051	0.4434	-35.9564	28.6814	11.7783
6	0.7666	0.1663	-0.3292	0.1974	-0.0131	0.6977	0.091	0.1332	-0.1982	-0.1165	-0.2201	-0.1373	0.3875	0.181	0.0408	0.6583	0.3703	0.0517	0.55	0.0342	0.5297	-21.0791	24.274	21.2825
7	0.72	0.033	-0.4234	1.288	-0.2116	1.0137	0.1156	0.1318	0.2619	-0.0492	-0.0453	-0.1427	-0.0007	0.3711	-0.1455	0.4291	0.2223	0.0328	0.5582	0.0809	0.5193	-17.9292	41.9438	21.4075
8	0.9886	-0.1989	-0.8367	0.5842	0.437	0.9336	0.2174	0.4924	0.2408	-0.2824	0.0726	-0.0808	-0.6446	0.1483	-0.0961	0.5577	0.1866	0.211	0.6144	0.2045	0.6367	-16.4717	51.8762	13.9064
9	0.5284	-0.2474	-0.1825	0.4068	-0.2942	0.5307	-0.0278	0.4328	-0.0502	-0.0038	-0.0025	0.0835	0.3596	-0.0311	0.0445	0.5271	0.2191	0.0667	0.4813	0.0574	0.5001	-24.9941	35.5225	22.6014
10	1.9064	-0.6928	-0.4904	1.2242	-0.4145	1.5281	-0.0788	-0.2681	-0.3774	0.153	0.0217	0.1839	0.3228	0.0837	0.0041	0.6522	0.2585	0.0236	0.44	0.0749	0.501	-26.3934	22.3402	35.7985
11	0.3683	-0.0008	-0.2313	0.9185	0.291	0.3594	-0.2287	-0.1681	-0.1875	0.1378	0.057	-0.3156	0.1468	0.1099	-0.5514	0.7561	0.5467	0.0918	0.5809	0.0703	0.8191	-12.2128	15.3485	28.572
12	1.9229	-1.0301	-0.071	1.4601	0.893	0.8515	0.0314	-0.5332	-0.629	0.0914	-0.0375	0.0257	0.7957	0.0241	-0.0028	0.8065	0.184	0.0613	0.4311	0.1196	0.6119	-31.0852	14.7443	37.2026
13	0.6692	0.2827	0.762	0.4811	-0.2009	1.589	0.1683	0.1911	-0.6504	0.075	-0.1689	0.3084	0.319	-0.2936	-0.0763	0.941	0.2546	0.1288	0.5961	-0.0731	0.6912	-30.594	5.8923	13.9168
14	0.6067	-0.0199	-0.1647	0.4141	0.6156	1.0393	0.1394	-0.3342	0.0709	0.0685	-0.2463	0.0899	-0.3247	-0.4212	0.0372	0.3423	0.0113	-0.0183	0.641	-0.0908	0.4521	-35.0291	40.2548	-37.8262
15	0.5905	0.1597	-0.0508	1.7697	0.1127	0.5424	0.0359	-0.5035	-0.0857	0.4371	-0.2246	0.0567	0.0085	-0.3799	0.1337	0.4483	-0.1093	-0.0043	0.9263	0.074	0.3708	-31.6217	27.4722	-12.3154
16	0.4913	-0.3508	0.0533	0.8233	-0.0258	0.9746	0.0232	-0.3296	-0.0527	0.0919	-0.1333	0.252	0.207	-0.7195	0.104	0.3764	-0.1557	0.0132	0.8404	-0.0573	0.4799	-39.7272	29.2898	-28.1783
17	0.3689	0.1586	-0.2031	0.6545	0.0748	1.0896	0.0478	-0.1166	0.3305	-0.0248	-0.0875	0.2971	-0.5013	-0.7965	-0.06	0.3982	0.2014	-0.0189	1.1202	-0.1517	0.5688	-49.582	46.5398	-35.6694
18	0.957	0.1414	-0.4412	1.3195	0.259	1.1222	-0.028	-0.4157	-0.0205	0.103	-0.1129	0.1624	0.0089	-0.6064	0.0822	0.2808	0.0181	-0.0538	0.7179	-0.0913	0.3982	-40.4156	35.4348	-39.8327
19	0.0577	-0.1161	0.0197	0.4149	-0.221	0.1953	0.0717	0.3059	-0.464	-0.173	0.1304	0.401	0.2385	-0.519	0.0828	0.3533	-0.313	-0.1284	1.262	-0.0035	0.7135	-51.4933	18.4555	-46.2072
20	1.2161	0.7134	-0.0787	1.3933	-0.3662	0.6191	0.2527	0.2032	-0.6049	-0.0222	-0.2472	-0.1644	0.8683	-0.0919	0.0014	0.5073	-0.0809	-0.0399	0.4043	-0.0943	0.4615	-30.9448	17.8847	-47.9299
21	0.2535	-0.1792	0.2755	0.3941	0.1159	1.2787	-0.1381	-0.0967	-0.364	-0.0635	-0.2424	-0.0743	0.4253	0.1745	0.2132	0.9123	-0.3751	-0.0492	0.9694	0.0646	0.7642	-39.5616	8.3325	-26.5901
22	1.9262	0.2794	0.2191	0.6444	-0.2556	0.8005	0.1116	-0.2358	0.3	0.0374	-0.1778	0.0523	-0.4281	-0.1271	0.0593	0.7229	-0.0163	0.0047	0.3637	-0.1398	0.4479	-9.796	73.209	-26.5441
23	1.8089	0.2157	0.1855	0.9045	-0.2057	0.5259	0.1585	-0.6384	0.2858	0.1445	-0.1779	0.119	-0.4752	-0.1934	-0.0072	0.6921	0.0004	0.0347	0.6587	-0.2707	0.5087	-16.734	72.4878	-16.8615

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 80 through 307 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 308 through 425 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 426 through 514 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 80 through 135 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 136 through 230 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 231 through 307 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 308 through 340 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 341 through 363 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 364 through 393 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 394 through 425 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 426 through 449 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 450 through 485 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 486 through 514 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 80 through 112 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 113 through 135 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 136 through 307 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 308 through 351 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 352 through 425 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 426 through 449 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 450 through 485 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 486 through 514 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 80 through 307 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 308 through 514 )

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