PDB-2on5: Structure of NaGST-2

ID or keywords:

Entry

Database: PDB / ID: 2on5

Title

Structure of NaGST-2

Components

Na Glutathione S-transferase 2

Keywords

TRANSFERASE / GST / hookworm / Necator

Function / homology

Function and homology information

glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function

Biological species

Necator americanus (New World hookworm)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Asojo, O.A. / Ngamelue, M. / Homma, H. / Goud, G. / Zhan, B. / Hotez, P.J.

Citation

Journal: Bmc Struct.Biol. / Year: 2007
Title: X-ray structures of Na-GST-1 and Na-GST-2 two glutathione s-transferase from the human hookworm Necator americanus
Authors: Asojo, O.A. / Homma, K. / Sedlacek, M. / Ngamelue, M. / Goud, G.N. / Zhan, B. / Deumic, V. / Asojo, O. / Hotez, P.J.

History

Deposition	Jan 23, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Dec 21, 2011	Group: Non-polymer description
Revision 1.3	Mar 21, 2012	Group: Non-polymer description
Revision 1.4	Aug 30, 2023	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_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2on5.cif.gz	385.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2on5.ent.gz	315.8 KB	Display	PDB format
PDBx/mmJSON format	2on5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2on5_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	2on5_full_validation.pdf.gz	2.4 MB	Display
Data in XML	2on5_validation.xml.gz	87.2 KB	Display
Data in CIF	2on5_validation.cif.gz	120.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/on/2on5 ftp://data.pdbj.org/pub/pdb/validation_reports/on/2on5	HTTPS FTP

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Related structure data

Related structure data	2on7C 1tw9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ecb-d 6n8u-1 4l5l-d 2c3n-1 2oad-d 2oac-d 5j5n-d 2c3t-1 3fdc-1 1ayx-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

2on7C

1tw9S

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (11) #255 - Mar 2021 Cisplatin and DNA similarity (11)

Deposited unit

A: Na Glutathione S-transferase 2

B: Na Glutathione S-transferase 2

C: Na Glutathione S-transferase 2

D: Na Glutathione S-transferase 2

E: Na Glutathione S-transferase 2

F: Na Glutathione S-transferase 2

G: Na Glutathione S-transferase 2

H: Na Glutathione S-transferase 2

hetero molecules

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

1

A: Na Glutathione S-transferase 2

G: Na Glutathione S-transferase 2

hetero molecules

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

2

B: Na Glutathione S-transferase 2

C: Na Glutathione S-transferase 2

hetero molecules

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

3

D: Na Glutathione S-transferase 2

F: Na Glutathione S-transferase 2

hetero molecules

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

4

E: Na Glutathione S-transferase 2

H: Na Glutathione S-transferase 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.916, 107.921, 166.990
Angle α, β, γ (deg.)	90.00, 90.02, 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 auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 5 / Auth seq-ID: 1 - 206 / Label seq-ID: 1 - 206

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

#1: Protein	Na Glutathione S-transferase 2 / NaGST-2 Mass: 23668.207 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Necator americanus (New World hookworm) Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / References: UniProt: D3U1A6*PLUS
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1771 / 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: 2.75 Å³/Da / Density % sol: 55.35 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2005 / Details: mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.82→33 Å / Num. all: 161446 / Num. obs: 142281 / % possible obs: 88.1 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / R_merge(I) obs: 0.073 / R_sym value: 0.062 / Net I/σ(I): 13.1
Reflection shell	Resolution: 1.82→1.89 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.489 / Mean I/σ(I) obs: 1.39 / R_sym value: 0.407 / % possible all: 50.7

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHASES		phasing
REFMAC	5.2	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TW9

1tw9

Resolution: 1.9→25 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.93 / SU B: 2.159 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22702	7090	5 %	RANDOM
R_work	0.17798	-	-	-
obs	0.1804	135157	88.13 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.494 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0 Å²	-0.34 Å²
2-	-	0.36 Å²	0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13400	0	464	1771	15635

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	14148
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.408	1.99	18896
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.477	5	1640
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.706	23.457	648
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.744	15	2432
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.553	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	1920
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10672
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	7491
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	9531
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	1593
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	0.222	0.2	85
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.115	0.2	38
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	0.851	1.5	8541
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.182	2	13208
X-RAY DIFFRACTION	r_scbond_it	2.283	3	6472
X-RAY DIFFRACTION	r_scangle_it	3.357	4.5	5688
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	824	medium positional	0.24	0.5
2	B	824	medium positional	0.24	0.5
3	C	824	medium positional	0.25	0.5
4	D	824	medium positional	0.19	0.5
5	E	824	medium positional	0.18	0.5
6	F	824	medium positional	0.12	0.5
7	G	824	medium positional	0.25	0.5
8	H	824	medium positional	0.13	0.5
1	A	851	loose positional	0.64	5
2	B	851	loose positional	0.58	5
3	C	851	loose positional	0.71	5
4	D	851	loose positional	0.57	5
5	E	851	loose positional	0.71	5
6	F	851	loose positional	0.68	5
7	G	851	loose positional	0.74	5
8	H	851	loose positional	0.54	5
1	A	824	medium thermal	1.88	2
2	B	824	medium thermal	1.83	2
3	C	824	medium thermal	1.06	2
4	D	824	medium thermal	1.79	2
5	E	824	medium thermal	1.75	2
6	F	824	medium thermal	1.37	2
7	G	824	medium thermal	1.03	2
8	H	824	medium thermal	1.31	2
1	A	851	loose thermal	2.73	10
2	B	851	loose thermal	2.65	10
3	C	851	loose thermal	2.08	10
4	D	851	loose thermal	2.64	10
5	E	851	loose thermal	2.83	10
6	F	851	loose thermal	2.16	10
7	G	851	loose thermal	2.16	10
8	H	851	loose thermal	2.1	10

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	396	-
R_work	0.234	8187	-
obs	-	-	72.41 %

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	0.4938	-0.1661	-0.0199	0.6401	-0.125	0.5862	-0.0076	-0.0559	-0.0126	-0.0282	0.0009	-0.051	-0.005	0.0338	0.0067	-0.0656	-0.0073	-0.0149	-0.0785	0.0027	-0.1194	28.664	2.008	42.945
2	0.6818	0.1911	0.0925	0.8437	-0.1067	0.7024	-0.0058	0.0814	0.0176	0.0106	-0.0048	-0.0436	0.0125	0.0285	0.0106	-0.0705	0.0118	-0.0117	-0.0757	0.0013	-0.1201	28.676	51.794	40.545
3	0.8406	0.2499	0.2786	0.7992	0.0545	0.7278	-0.01	-0.0059	0.1445	0.0943	-0.0014	0.1233	-0.0238	-0.0419	0.0114	-0.0619	0.0076	0.0066	-0.0987	0.0056	-0.0766	8.168	62.542	51.374
4	1.238	-0.055	-0.4642	0.7147	0.457	1.8525	-0.0519	-0.2241	-0.1455	0.0793	-0.0291	0.0459	0.217	0.0086	0.0811	-0.0291	-0.0046	-0.0148	-0.0445	0.0276	-0.1096	14.997	28.834	76.24
5	1.1252	0.0628	0.4059	0.6586	0.4206	1.7449	-0.0472	0.2124	0.1306	-0.0742	-0.0286	0.0285	-0.2141	-0.013	0.0758	-0.0268	0.0057	-0.0164	-0.0466	0.0259	-0.1099	15.01	24.963	7.238
6	0.7978	-0.3133	-0.0628	0.6663	0.0785	0.7653	0.0109	-0.1286	0.041	0.0111	-0.0064	-0.084	-0.0916	0.2025	-0.0045	-0.0418	-0.0447	-0.0171	0.0219	-0.0052	-0.1212	35.364	43.238	81.408
7	0.7406	-0.2242	-0.3427	0.8323	0.0293	0.7655	-0.0158	0.0115	-0.1431	-0.0923	-0.0032	0.117	0.0376	-0.0395	0.019	-0.0631	-0.0072	-0.0437	-0.0927	0.0036	-0.0778	8.192	-8.728	32.089
8	0.7534	0.3529	0.0543	0.7161	0.1161	0.693	-0.0021	0.1252	-0.0351	-0.0151	0.0041	-0.0689	0.0856	0.1954	-0.002	-0.0495	0.0428	-0.0137	0.027	-0.0001	-0.1197	35.373	10.545	2.085

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	1 - 206	1 - 206
2	X-RAY DIFFRACTION	2	B	B	1 - 206	1 - 206
3	X-RAY DIFFRACTION	3	C	C	1 - 206	1 - 206
4	X-RAY DIFFRACTION	4	D	D	1 - 206	1 - 206
5	X-RAY DIFFRACTION	5	E	E	1 - 206	1 - 206
6	X-RAY DIFFRACTION	6	F	F	1 - 206	1 - 206
7	X-RAY DIFFRACTION	7	G	G	1 - 206	1 - 206
8	X-RAY DIFFRACTION	8	H	H	1 - 206	1 - 206

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