PDB-8fbz: Crystal Structure of apo human Glutathione Synthetase Y270E

ID or keywords:

Entry

Database: PDB / ID: 8fbz

Title

Crystal Structure of apo human Glutathione Synthetase Y270E

Components

Glutathione synthetase

Keywords

BIOSYNTHETIC PROTEIN / Glutathione Synthesis ATPase

Function / homology

Function and homology information

Defective GSS causes GSS deficiency / glutathione synthase / glutathione synthase activity / Glutathione synthesis and recycling / glutathione binding / amino acid metabolic process / response to cadmium ion / nervous system development / response to oxidative stress / magnesium ion binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.59 Å

Authors

Stanford, S.M. / Santelli, E. / Sankaran, B. / Murali, R. / Bottini, N.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	DK106233	United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	HL152717	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	CA245621	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM124169	United States

Citation

Journal: Sci Adv / Year: 2024
Title: Targeting prostate tumor low-molecular weight tyrosine phosphatase for oxidation-sensitizing therapy.
Authors: Stanford, S.M. / Nguyen, T.P. / Chang, J. / Zhao, Z. / Hackman, G.L. / Santelli, E. / Sanders, C.M. / Katiki, M. / Dondossola, E. / Brauer, B.L. / Diaz, M.A. / Zhan, Y. / Ramsey, S.H. / ...

History

Deposition	Nov 30, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8fbz.cif.gz	353.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8fbz.ent.gz	275 KB	Display	PDB format
PDBx/mmJSON format	8fbz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fb/8fbz ftp://data.pdbj.org/pub/pdb/validation_reports/fb/8fbz	HTTPS FTP

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Related structure data

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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #192 - Dec 2015 Vancomycin similarity (1) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1)

Deposited unit

B: Glutathione synthetase

A: Glutathione synthetase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	80.834, 94.051, 125.122
Angle α, β, γ (deg.)	90.000, 92.522, 90.000
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	B-1059- HOH
2	1	A-1002- HOH
3	1	A-1070- HOH
4	1	A-1120- HOH

#1: Protein	Glutathione synthetase / GSH synthetase / GSH-S / Glutathione synthase Mass: 52691.836 Da / Num. of mol.: 2 / Mutation: Y270E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSS / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P48637, glutathione synthase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1046 / 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: 2.33 Å³/Da / Density % sol: 47.11 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, PEG400, ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 3, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.59→47.07 Å / Num. obs: 123489 / % possible obs: 98.6 % / Redundancy: 4.3 % / CC_1/2: 0.996 / R_merge(I) obs: 0.093 / R_pim(I) all: 0.066 / R_rim(I) all: 0.106 / Net I/σ(I): 10.1
Reflection shell	Resolution: 1.59→1.63 Å / R_merge(I) obs: 0.687 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5993 / CC_1/2: 0.74 / R_pim(I) all: 0.359 / R_rim(I) all: 0.778

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.59→47.07 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.953 / SU B: 3.282 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1888	6675	5.408 %
R_work	0.1599	116752	-
all	0.161	-	-
obs	-	123427	98.42 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.175 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.139 Å²	-0 Å²	0.073 Å²
2-	-	-0.899 Å²	0 Å²
3-	-	-	-0.245 Å²

Refinement step

Cycle: LAST / Resolution: 1.59→47.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7186	0	36	1046	8268

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	7433
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	7254
X-RAY DIFFRACTION	r_angle_refined_deg	1.357	1.638	10078
X-RAY DIFFRACTION	r_angle_other_deg	1.375	1.576	16695
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.128	5	944
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.596	22.353	408
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.644	15	1332
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.62	15	59
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	959
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8447
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1687
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	1506
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.177	0.2	6694
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	3580
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	3432
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	788
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.077	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.239	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.185	0.2	85
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.144	0.2	32
X-RAY DIFFRACTION	r_mcbond_it	2.136	1.486	3701
X-RAY DIFFRACTION	r_mcbond_other	2.131	1.485	3700
X-RAY DIFFRACTION	r_mcangle_it	2.958	2.219	4622
X-RAY DIFFRACTION	r_mcangle_other	2.96	2.219	4623
X-RAY DIFFRACTION	r_scbond_it	4.33	1.961	3732
X-RAY DIFFRACTION	r_scbond_other	4.33	1.962	3733
X-RAY DIFFRACTION	r_scangle_it	6.37	2.756	5440
X-RAY DIFFRACTION	r_scangle_other	6.369	2.756	5441
X-RAY DIFFRACTION	r_lrange_it	7.894	20.71	8598
X-RAY DIFFRACTION	r_lrange_other	7.672	19.446	8279

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 (%)
1.59-1.631	0.26	497	0.233	8526	X-RAY DIFFRACTION	97.7044
1.631-1.676	0.245	420	0.213	8470	X-RAY DIFFRACTION	98.8547
1.676-1.724	0.21	429	0.194	8243	X-RAY DIFFRACTION	98.9954
1.724-1.777	0.225	462	0.182	7961	X-RAY DIFFRACTION	99.0708
1.777-1.836	0.217	449	0.178	7713	X-RAY DIFFRACTION	99.1135
1.836-1.9	0.21	397	0.175	7512	X-RAY DIFFRACTION	99.0234
1.9-1.972	0.204	471	0.161	7169	X-RAY DIFFRACTION	99.015
1.972-2.052	0.189	437	0.148	6891	X-RAY DIFFRACTION	99.4706
2.052-2.143	0.171	449	0.142	6599	X-RAY DIFFRACTION	98.7807
2.143-2.247	0.168	383	0.141	6352	X-RAY DIFFRACTION	99.0878
2.247-2.369	0.176	377	0.144	6044	X-RAY DIFFRACTION	98.9521
2.369-2.512	0.165	361	0.137	5696	X-RAY DIFFRACTION	99.23
2.512-2.685	0.176	312	0.14	5399	X-RAY DIFFRACTION	98.6526
2.685-2.899	0.179	280	0.144	4987	X-RAY DIFFRACTION	97.936
2.899-3.175	0.17	253	0.146	4568	X-RAY DIFFRACTION	97.4727
3.175-3.548	0.162	188	0.153	4129	X-RAY DIFFRACTION	96.5988
3.548-4.094	0.186	159	0.149	3644	X-RAY DIFFRACTION	95.5288
4.094-5.005	0.171	155	0.157	3049	X-RAY DIFFRACTION	95.2721
5.005-7.043	0.236	125	0.205	2395	X-RAY DIFFRACTION	96.3671
7.043-47.07	0.264	71	0.201	1405	X-RAY DIFFRACTION	97.8131

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	0.1853	-0.0145	-0.017	0.3289	0.0246	0.2324	-0.0164	0.0162	-0.024	-0.0029	0.0065	-0.0095	0.0327	-0.0129	0.0099	0.006	-0.004	0.0043	0.0059	-0.0067	0.0078	18.0891	-81.867	-14.3694
2	0.2146	0.0192	-0.0133	0.3127	0.0512	0.1751	-0.0089	-0.0095	0.0294	-0.0061	0.0025	0.0022	-0.0217	-0.0043	0.0064	0.0042	0.0025	-0.0042	0.0039	-0.0042	0.0083	16.6227	-43.7946	14.0924

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	B	5 - 474
2	X-RAY DIFFRACTION	2	ALL	A	3 - 474

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