PDB-2gwc: Crystal structure of plant glutamate cysteine ligase in complex w...

ID or keywords:

Entry

Database: PDB / ID: 2gwc

Title

Crystal structure of plant glutamate cysteine ligase in complex with a transition state analogue

Components

Glutamate cysteine ligase

Keywords

LIGASE / disulfide bridges / glutathione biosynthesis / beta-hairpin / redox regulation

Function / homology

Function and homology information

oxoacid metabolic process / glutamate-cysteine ligase / glutamate-cysteine ligase activity / glutathione biosynthetic process / chloroplast / ATP binding
Similarity search - Function

Biological species

Brassica juncea (brown mustard)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.18 Å

Authors

Hothorn, M. / Wachter, A. / Gromes, R. / Stuwe, T. / Rausch, T. / Scheffzek, K.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Structural basis for the redox control of plant glutamate cysteine ligase.
Authors: Hothorn, M. / Wachter, A. / Gromes, R. / Stuwe, T. / Rausch, T. / Scheffzek, K.

History

Deposition	May 4, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 20, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 2.0	Oct 3, 2018	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary Category: chem_comp / entity / pdbx_entity_nonpoly Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2gwc.cif.gz	694.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2gwc.ent.gz	598.2 KB	Display	PDB format
PDBx/mmJSON format	2gwc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2gwc_validation.pdf.gz	514.8 KB	Display	wwPDB validaton report
Full document	2gwc_full_validation.pdf.gz	548.1 KB	Display
Data in XML	2gwc_validation.xml.gz	123.7 KB	Display
Data in CIF	2gwc_validation.cif.gz	175.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gw/2gwc ftp://data.pdbj.org/pub/pdb/validation_reports/gw/2gwc	HTTPS FTP

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Related structure data

Related structure data	2gwdC C: citing same article (ref.)
Similar structure data	6gmo-d 5ioj-d 4q2r-d 3jq3-1 1i0e-2 5rb5-d 3jpz-d 5hrm-2 1xwk-d 4xrg-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

2gwdC

C: citing same article (ref.)

Similar structure data

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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

B: Glutamate cysteine ligase

C: Glutamate cysteine ligase

D: Glutamate cysteine ligase

E: Glutamate cysteine ligase

F: Glutamate cysteine ligase

G: Glutamate cysteine ligase

H: Glutamate cysteine ligase

hetero molecules

417 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutamate cysteine ligase

B: Glutamate cysteine ligase

hetero molecules

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

2

C: Glutamate cysteine ligase

D: Glutamate cysteine ligase

hetero molecules

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

3

E: Glutamate cysteine ligase

F: Glutamate cysteine ligase

hetero molecules

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

4

G: Glutamate cysteine ligase

H: Glutamate cysteine ligase

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.040, 198.920, 114.970
Angle α, β, γ (deg.)	90.00, 99.66, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: PRO / End label comp-ID: TYR / Refine code: 2 / Auth seq-ID: 80 - 514 / Label seq-ID: 15 - 449

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H

Details

The oxidized state of the enzyme is associated with a dimeric configuration. The asymmetric unit contains four dimers (A-B, C-D, E-F, G-H)

#1: Protein	Glutamate cysteine ligase / Gamma-glutamylcysteine synthetase / Gamma-ECS / GCS Mass: 51818.281 Da / Num. of mol.: 8 / Fragment: glutamate cysteine ligase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brassica juncea (brown mustard) / Gene: GSH1 / Plasmid: pETM20 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami (DE3) / References: UniProt: O23736, glutamate-cysteine ligase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-BSC / (2S)-2-amino-4-(S-butylsulfonimidoyl)butanoic acid / L-BUTHIONINE-[S,R]-SULFOXIMINE Mass: 222.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₃S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1017 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.6 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% PEG 3350, 0.2 M magnesium acetate tetrahydrate, 0.1 M tricine, 0.01 M L-buthionine(S,R)sulfoximine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.9797, 0.9778, 0,.9737

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2005

Radiation

Monochromator: transparent diamond monochromators / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9797	1
2	0.9778	1
3	0	1
4	0.9737	1

Reflection

Resolution: 2.18→99.5 Å / Num. obs: 197271 / % possible obs: 95.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / R_sym value: 0.104 / Net I/σ(I): 13.6

Reflection shell

Resolution: 2.18→2.27 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 40871 / R_sym value: 0.457 / % possible all: 89.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
ADSC		data collection
XDS		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.18→99.5 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.915 / SU B: 12.676 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.283 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24126	9951	5 %	RANDOM
R_work	0.19787	-	-	-
all	0.2	197621	-	-
obs	0.2	187310	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.442 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.04 Å²	0 Å²	0.01 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.18→99.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28002	0	120	1017	29139

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	28892
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	26219
X-RAY DIFFRACTION	r_angle_refined_deg	1.479	1.971	39093
X-RAY DIFFRACTION	r_angle_other_deg	0.916	3.001	60896
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.892	5	3511
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.273	23.759	1362
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.721	15	5037
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.219	15	209
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	4144
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	31973
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	6032
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	5756
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	26506
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	13808
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	16204
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	1153
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.062	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.073	0.2	5
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.219	0.2	36
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.23	0.2	197
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.221	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.09	1.5	21523
X-RAY DIFFRACTION	r_mcbond_other	0.278	1.5	7133
X-RAY DIFFRACTION	r_mcangle_it	0.88	2	28081
X-RAY DIFFRACTION	r_scbond_it	2.262	3	13176
X-RAY DIFFRACTION	r_scangle_it	3.064	4.5	11001

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2545	tight positional	0.05	0.05
2	B	2545	tight positional	0.05	0.05
3	C	2545	tight positional	0.05	0.05
4	D	2545	tight positional	0.06	0.05
5	E	2545	tight positional	0.06	0.05
6	F	2545	tight positional	0.05	0.05
7	G	2545	tight positional	0.05	0.05
8	H	2545	tight positional	0.05	0.05
1	A	4146	medium positional	0.22	0.5
2	B	4146	medium positional	0.2	0.5
3	C	4146	medium positional	0.19	0.5
4	D	4146	medium positional	0.21	0.5
5	E	4146	medium positional	0.2	0.5
6	F	4146	medium positional	0.21	0.5
7	G	4146	medium positional	0.2	0.5
8	H	4146	medium positional	0.19	0.5
1	A	2545	tight thermal	0.11	0.5
2	B	2545	tight thermal	0.1	0.5
3	C	2545	tight thermal	0.1	0.5
4	D	2545	tight thermal	0.11	0.5
5	E	2545	tight thermal	0.11	0.5
6	F	2545	tight thermal	0.1	0.5
7	G	2545	tight thermal	0.11	0.5
8	H	2545	tight thermal	0.1	0.5
1	A	4146	medium thermal	0.48	2
2	B	4146	medium thermal	0.46	2
3	C	4146	medium thermal	0.44	2
4	D	4146	medium thermal	0.49	2
5	E	4146	medium thermal	0.5	2
6	F	4146	medium thermal	0.45	2
7	G	4146	medium thermal	0.46	2
8	H	4146	medium thermal	0.46	2

LS refinement shell

Resolution: 2.18→2.237 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	713	-
R_work	0.268	13142	-
obs	-	13142	100 %

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	1.1408	-0.0594	-0.0034	0.4771	0.1013	0.2874	-0.0066	0.0154	0.0228	-0.0576	0.0053	-0.0618	-0.0755	-0.0261	0.0013	-0.0228	-0.0083	0.0043	-0.092	0.0062	-0.0803	30.5546	16.4389	35.921
2	0.9968	0.0192	-0.0353	0.9709	-0.1565	0.3671	-0.0105	-0.0269	-0.0973	-0.0072	0.007	0.0689	0.0255	-0.057	0.0035	-0.0537	-0.013	0.0033	-0.0323	0.0143	-0.0487	-9.2114	-2.9946	51.0521
3	0.8863	0.1118	-0.0947	0.8419	-0.0305	0.4272	-0.0243	-0.0005	0.0415	-0.0696	0.0333	-0.0586	-0.0354	0.0807	-0.009	-0.0647	-0.0109	0.0065	-0.0232	0.034	-0.0398	41.6304	-32.5162	54.6724
4	1.0531	-0.0996	0.1906	0.6502	-0.1813	0.2371	-0.0315	0.0825	-0.0684	-0.0387	0.0305	0.0905	0.0561	-0.0282	0.001	-0.0283	-0.0096	0.0068	-0.0365	0.0103	-0.0346	1.8901	-54.7254	44.6333
5	1.0196	0.0979	0.011	0.9235	-0.0478	0.4624	-0.0165	0.07	-0.0887	-0.0635	0.01	0.0473	0.0177	-0.0173	0.0065	-0.0613	-0.0061	-0.0095	-0.0609	-0.0021	-0.0882	0.6618	-1.9769	-6.0314
6	1.2414	0.0243	0.0473	0.6877	-0.0218	0.2442	0.0073	0.1139	0.0852	-0.0899	-0.0012	-0.0574	-0.058	-0.0347	-0.006	-0.02	-0.0082	0.006	-0.039	0.0001	-0.0956	40.4046	17.9222	-20.7116
7	0.9624	0.2681	0.1798	0.7931	0.3036	0.3196	0.026	0.0344	-0.1193	0.0737	0.0103	-0.1905	0.0896	0.0542	-0.0363	-0.0274	0.0083	-0.0383	-0.0909	0.011	0.002	-11.9824	45.72	13.4761
8	1.1868	-0.2177	-0.1422	0.7734	-0.0077	0.3927	0.0306	0.0495	-0.0315	0.0295	-0.0393	0.0615	-0.0517	-0.1043	0.0087	-0.0574	0.0127	-0.0135	-0.0398	-0.0036	-0.0501	-51.5753	67.9227	3.0432

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	80 - 514	15 - 449
2	X-RAY DIFFRACTION	2	B	B	80 - 514	15 - 449
3	X-RAY DIFFRACTION	3	C	C	80 - 514	15 - 449
4	X-RAY DIFFRACTION	4	D	D	80 - 514	15 - 449
5	X-RAY DIFFRACTION	5	E	E	80 - 514	15 - 449
6	X-RAY DIFFRACTION	6	F	F	80 - 514	15 - 449
7	X-RAY DIFFRACTION	7	G	G	80 - 514	15 - 449
8	X-RAY DIFFRACTION	8	H	H	80 - 514	15 - 449

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