PDB-2wyo: Trypanosoma brucei glutathione synthetase

ID or keywords:

Entry

Database: PDB / ID: 2wyo

Title

Trypanosoma brucei glutathione synthetase

Components

GLUTATHIONE SYNTHETASE

Keywords

LIGASE / ATP-GRASP

Function / homology

Function and homology information

glutathione synthase /

glutathione synthase activity /

glutathione binding /

nucleolus / magnesium ion binding / protein homodimerization activity /

ATP binding /

cytosol /

cytoplasm
Similarity search - Function

Biological species

TRYPANOSOMA BRUCEI (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.15 Å

Authors

Fyfe, P.K. / Alphey, M.S. / Hunter, W.N.

Citation

Journal: Mol.Biochem.Parasitol. / Year: 2010
Title: Structure of Trypanosoma Brucei Glutathione Synthetase; Domain and Loop Alterations in the Catalytic Cycle of a Highly Conserved Enzyme.
Authors: Fyfe, P.K. / Alphey, M.S. / Hunter, W.N.

History

Deposition	Nov 17, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 7, 2011	Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wyo.cif.gz	387.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2wyo.ent.gz	315.3 KB	Display	PDB format
PDBx/mmJSON format	2wyo.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/wy/2wyo ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wyo	HTTPS FTP

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Related structure data

Related structure data	1m0wS S: Starting model for refinement
Similar structure data	2hvg-d 4e8c-d 2qga-d 4axd-1 4mad-d 6mwr-d 5y4l-d 6bxj-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) 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 (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #192 - Dec 2015 Vancomycin similarity (1) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: GLUTATHIONE SYNTHETASE

B: GLUTATHIONE SYNTHETASE

C: GLUTATHIONE SYNTHETASE

D: GLUTATHIONE SYNTHETASE

hetero molecules

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

1

C: GLUTATHIONE SYNTHETASE

D: GLUTATHIONE SYNTHETASE

hetero molecules

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

2

A: GLUTATHIONE SYNTHETASE

B: GLUTATHIONE SYNTHETASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.590, 125.150, 243.170
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 4

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	GLU	GLU	A	A	114 - 125	121 - 132
2	1	1	MET	MET	GLU	GLU	B	B	114 - 125	121 - 132
3	1	1	MET	MET	GLU	GLU	C	C	114 - 125	121 - 132
4	1	1	MET	MET	GLU	GLU	D	D	114 - 125	121 - 132
1	2	1	MET	MET	ALA	ALA	A	A	493 - 506	500 - 513
2	2	1	MET	MET	ALA	ALA	B	B	493 - 506	500 - 513
3	2	1	MET	MET	ALA	ALA	C	C	493 - 506	500 - 513
4	2	1	MET	MET	ALA	ALA	D	D	493 - 506	500 - 513
1	3	1	LEU	LEU	PRO	PRO	A	A	520 - 533	527 - 540
2	3	1	LEU	LEU	PRO	PRO	B	B	520 - 533	527 - 540
3	3	1	LEU	LEU	PRO	PRO	C	C	520 - 533	527 - 540
4	3	1	LEU	LEU	PRO	PRO	D	D	520 - 533	527 - 540
1	4	1	GLY	GLY	ARG	ARG	A	A	52 - 73	59 - 80
2	4	1	GLY	GLY	ARG	ARG	B	B	52 - 73	59 - 80
3	4	1	GLY	GLY	ARG	ARG	C	C	52 - 73	59 - 80
4	4	1	GLY	GLY	ARG	ARG	D	D	52 - 73	59 - 80
1	1	2	LEU	LEU	LYS	LYS	A	A	154 - 174	161 - 181
2	1	2	LEU	LEU	LYS	LYS	B	B	154 - 174	161 - 181
3	1	2	LEU	LEU	LYS	LYS	C	C	154 - 174	161 - 181
4	1	2	LEU	LEU	LYS	LYS	D	D	154 - 174	161 - 181
1	1	3	SER	SER	GLN	GLN	A	A	203 - 221	210 - 228
2	1	3	SER	SER	GLN	GLN	B	B	203 - 221	210 - 228
3	1	3	SER	SER	GLN	GLN	C	C	203 - 221	210 - 228
4	1	3	SER	SER	GLN	GLN	D	D	203 - 221	210 - 228
1	1	4	VAL	VAL	ILE	ILE	A	A	396 - 471	403 - 478
2	1	4	VAL	VAL	ILE	ILE	B	B	396 - 471	403 - 478
3	1	4	VAL	VAL	ILE	ILE	C	C	396 - 471	403 - 478
4	1	4	VAL	VAL	ILE	ILE	D	D	396 - 471	403 - 478

NCS ensembles :

ID
1
2
3
4

#1: Protein	GLUTATHIONE SYNTHETASE / Mass: 62231.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q57UN0, glutathione synthase
#2: Chemical	ChemComp-GSH / GLUTATHIONE / Glutathione Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.9 Å³/Da / Density % sol: 58 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.15→39.5 Å / Num. obs: 49689 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / B_iso Wilson estimate: 77.9 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 9
Reflection shell	Resolution: 3.15→3.32 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0097	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M0W

1m0w

Resolution: 3.15→39.46 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.87 / SU B: 48.843 / SU ML: 0.395 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27671	2483	5 %	RANDOM
R_work	0.20258	-	-	-
obs	0.2063	47141	99.86 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.247 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.91 Å²	0 Å²	0 Å²
2-	-	-0.16 Å²	0 Å²
3-	-	-	-3.75 Å²

Refinement step

Cycle: LAST / Resolution: 3.15→39.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15545	0	115	22	15682

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	15980
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	10790
X-RAY DIFFRACTION	r_angle_refined_deg	1.426	1.967	21656
X-RAY DIFFRACTION	r_angle_other_deg	0.917	3	26263
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.324	5	1976
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.069	23.766	709
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.521	15	2681
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.516	15	114
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	2453
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	17681
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3218
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.426	1.5	9929
X-RAY DIFFRACTION	r_mcbond_other	0.061	1.5	4035
X-RAY DIFFRACTION	r_mcangle_it	0.816	2	15985
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.034	3	6051
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.843	4.5	5671
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	822	medium positional	0.35	0.5
1	4	D	822	medium positional	0.36	0.5
1	3	C	822	medium positional	0.43	0.5
1	2	B	822	medium positional	0.35	0.5
2	1	A	287	medium positional	0.49	0.5
2	4	D	287	medium positional	0.3	0.5
2	3	C	287	medium positional	0.41	0.5
2	2	B	287	medium positional	0.35	0.5
3	1	A	233	medium positional	0.55	0.5
3	4	D	233	medium positional	0.34	0.5
3	3	C	233	medium positional	0.47	0.5
3	2	B	233	medium positional	0.33	0.5
4	1	A	346	medium positional	0.97	0.5
4	4	D	346	medium positional	0.8	0.5
4	3	C	346	medium positional	0.99	0.5
4	2	B	346	medium positional	0.73	0.5
1	1	A	822	medium thermal	0.41	2
1	4	D	822	medium thermal	0.35	2
1	3	C	822	medium thermal	0.39	2
1	2	B	822	medium thermal	0.38	2
2	1	A	287	medium thermal	0.41	2
2	4	D	287	medium thermal	0.41	2
2	3	C	287	medium thermal	0.38	2
2	2	B	287	medium thermal	0.36	2
3	1	A	233	medium thermal	0.54	2
3	4	D	233	medium thermal	0.44	2
3	3	C	233	medium thermal	0.98	2
3	2	B	233	medium thermal	0.5	2
4	1	A	346	medium thermal	0.22	2
4	4	D	346	medium thermal	0.25	2
4	3	C	346	medium thermal	0.25	2
4	2	B	346	medium thermal	0.25	2

LS refinement shell

Resolution: 3.15→3.231 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	179	-
R_work	0.251	3405	-
obs	-	-	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	3.1225	2.4262	0.8763	3.9905	0.3	1.9632	0.1603	-0.3552	0.1117	0.6423	-0.0739	0.0063	-0.0593	-0.0292	-0.0864	0.3281	0.0716	-0.1425	0.1423	0.0418	0.2489	-33.5998	23.6348	-28.9719
2	2.8305	0.9144	-0.1108	2.703	-0.2253	3.3817	-0.064	0.1309	0.2363	0.2786	0.0718	-0.1324	-0.209	0.4939	-0.0078	0.3231	-0.071	-0.2242	0.0947	0.0072	0.3997	-22.4912	35.8178	-35.6836
3	2.9847	1.7611	2.9399	5.3554	2.8183	5.7634	0.0704	-0.3752	-0.1018	1.4072	0.2198	-1.438	-0.1794	0.9597	-0.2902	1.1032	-0.0994	-0.3911	0.8429	0.0165	0.9157	-23.5373	15.5207	-10.5408
4	6.2678	6.13	-1.2691	6.835	-1.4133	2.0518	0.1266	-0.2595	0.6788	0.4394	0.1375	0.4179	-0.3065	-0.0226	-0.2641	0.4805	0.0395	-0.2246	0.2226	-0.1033	0.3096	-33.5288	32.2872	-27.8334
5	3.6846	-0.6477	-1.4033	2.1403	0.686	2.7262	0.0964	-0.3964	0.4102	0.1375	0.0636	-0.0998	-0.4468	0.2436	-0.1601	0.1307	-0.0249	-0.0268	0.0643	-0.0657	0.1103	-34.6206	-5.2775	6.8136
6	5.4331	-0.9886	-1.7039	1.6606	0.4772	2.5073	-0.0307	-0.1862	-0.1011	0.2233	0.0788	0.2552	0.0002	-0.0374	-0.0481	0.0445	-0.0012	0.0216	0.0442	0.0227	0.069	-41.5524	-12.4383	4.7605
7	3.1933	-0.2528	0.083	2.7866	-0.1117	4.563	0.0621	-0.1529	0.6251	0.1458	0.0766	0.1457	-0.7791	-0.2781	-0.1387	0.1423	0.0561	0.0439	0.1047	-0.0397	0.2359	-50.6602	0.5465	4.9797
8	5.1158	-0.5953	-0.3265	2.2832	0.0546	3.4148	-0.1065	-1.1089	0.9164	0.6832	0.1807	-0.2289	-0.3838	0.4542	-0.0742	0.2584	-0.0077	-0.0419	0.3009	-0.1858	0.2212	-33.6271	-6.0892	15.743
9	2.4075	-1.4006	-0.2673	2.4154	0.1229	1.3148	0.2785	0.4194	0.094	-0.6257	-0.2527	-0.0373	-0.2732	0.0653	-0.0258	0.2267	0.0043	-0.01	0.1551	0.0561	0.0359	-26.9402	-18.6938	-31.6178
10	16.8306	-9.918	1.5495	8.7851	-0.8788	2.5044	0.471	-1.4212	-1.6276	-0.4913	0.2823	1.6168	0.0691	-1.0552	-0.7533	0.145	-0.0577	-0.073	0.5995	0.2356	0.4713	-35.8493	-25.0833	-23.132
11	2.7256	-0.5354	0.7791	2.7006	-0.2256	3.4031	0.0774	0.3887	0.3598	-0.4226	-0.0969	-0.423	-0.3705	0.4668	0.0194	0.1193	-0.0234	0.0745	0.131	0.0506	0.156	-9.4812	-25.9674	-27.4794
12	3.8551	-1.6924	-0.2504	2.4342	1.3926	3.3987	0.4456	1.1348	0.4126	-1.1988	-0.3677	-0.2365	-0.8177	0.0543	-0.0779	0.6768	0.0156	0.0469	0.4294	0.0925	0.2425	-27.8882	-18.7307	-40.8931
13	4.1556	0.9493	1.4617	1.2616	0.4931	3.2846	0.1594	0.6831	-0.3148	-0.4056	0.053	-0.1279	0.4876	0.331	-0.2125	0.4464	0.0662	-0.1371	0.1799	-0.0533	0.2315	-45.2639	11.9926	-68.8819
14	6.8725	4.6962	2.7881	3.6468	2.0639	4.8928	-0.3872	0.6562	0.5928	-0.7105	0.1607	0.2475	-0.6126	0.5517	0.2265	0.581	0.1913	0.0055	0.348	0.1706	0.3221	-37.6176	28.2349	-66.7549
15	2.5678	-0.4051	1.1931	2.4592	-0.8722	6.1249	0.2549	0.0412	-0.5251	-0.38	0.0288	0.1474	1.1403	-0.2501	-0.2837	0.359	-0.071	-0.2193	0.12	-0.005	0.3411	-56.1114	5.3709	-61.2257
16	3.2868	0.5619	0.8549	3.2759	-0.1194	5.3328	-0.066	1.3075	-0.7297	-1.1714	0.18	-0.343	0.476	0.8761	-0.114	0.7227	-0.0426	-0.093	0.7306	-0.1237	0.3969	-43.9663	14.6207	-78.1973

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-6 - 184
2	X-RAY DIFFRACTION	2	A	185 - 395
3	X-RAY DIFFRACTION	3	A	396 - 493
4	X-RAY DIFFRACTION	4	A	494 - 555
5	X-RAY DIFFRACTION	5	D	-1 - 101
6	X-RAY DIFFRACTION	6	D	102 - 234
7	X-RAY DIFFRACTION	7	D	247 - 405
8	X-RAY DIFFRACTION	8	D	406 - 555
9	X-RAY DIFFRACTION	9	C	-1 - 174
10	X-RAY DIFFRACTION	10	C	175 - 221
11	X-RAY DIFFRACTION	11	C	222 - 403
12	X-RAY DIFFRACTION	12	C	404 - 555
13	X-RAY DIFFRACTION	13	B	0 - 127
14	X-RAY DIFFRACTION	14	B	138 - 186
15	X-RAY DIFFRACTION	15	B	187 - 391
16	X-RAY DIFFRACTION	16	B	392 - 555

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