PDB-4hi7: Crystal structure of glutathione transferase homolog from drosoph...

ID or keywords:

Entry

Database: PDB / ID: 4hi7

Title

Crystal structure of glutathione transferase homolog from drosophilia mojavensis, TARGET EFI-501819, with bound glutathione

Components

GI20122

Keywords

UNKNOWN FUNCTION / GST / glutathione S-transferase / enzyme function initiative / EFI / Structural Genomics

Function / homology

Function and homology information

glutathione transferase activity / glutathione metabolic process
Similarity search - Function

Biological species

Drosophila mojavensis (fry)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.25 Å

Authors

Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...

Citation

Journal: To be Published
Title: Crystal structure of glutathione transferase homolog from drosophilia mojavensis, TARGET EFI-501819, with bound glutathione
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...

History

Deposition	Oct 11, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	4hi7.cif.gz	198 KB	Display	PDBx/mmCIF format
PDB format	pdb4hi7.ent.gz	157.4 KB	Display	PDB format
PDBx/mmJSON format	4hi7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4hi7_validation.pdf.gz	971.3 KB	Display	wwPDB validaton report
Full document	4hi7_full_validation.pdf.gz	972.2 KB	Display
Data in XML	4hi7_validation.xml.gz	24.7 KB	Display
Data in CIF	4hi7_validation.cif.gz	38.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hi/4hi7 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/4hi7	HTTPS FTP

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Related structure data

Related structure data	2il3S S: Starting model for refinement
Similar structure data	4yh2-2 4pnf-2 4gci-d 2vcq-2 4q5r-1 4edz-1 2imk-d 2yxv-2 4png-d 6f05-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: EFI-501819

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (10) #255 - Mar 2021 Cisplatin and DNA similarity (8)

Deposited unit

A: GI20122

B: GI20122

hetero molecules

51.7 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)	50.700, 50.700, 289.473
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-710- HOH

#1: Protein	GI20122 / GLUTATHIONE TRANSFERASE HOMOLOG Mass: 25556.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila mojavensis (fry) / Gene: GI20122, Dmoj\GI20122, Dmoj_GI20122 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4KM86
#2: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.1 Å³/Da / Density % sol: 41.46 %
Crystal grow	Temperature: 298 K / Method: sitting drop vapor diffution / pH: 6.5 Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl), Reservoir (0.2 M NaCl, 0.1 M Tris-CL pH 6.5, 30% PEG3000), Cryoprotection (reservoir + 20% ethylene glycol), sitting drop vapor diffution, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 13, 2012 / Details: MIRRORS

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.25→96.491 Å / Num. all: 116694 / Num. obs: 116694 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / B_iso Wilson estimate: 8.3 Å² / R_merge(I) obs: 0.073 / R_sym value: 0.073 / Net I/σ(I): 10.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.25-1.32	3.5	0.457	1.7	55616	15979	0.457	91.6
1.32-1.4	3.8	0.348	2.2	60178	15675	0.348	94.5
1.4-1.49	4.1	0.259	3	60351	14857	0.259	95.4
1.49-1.61	4.3	0.179	4.2	60132	14029	0.179	96.6
1.61-1.77	4.5	0.132	5.5	59030	13062	0.132	97.3
1.77-1.98	4.8	0.102	6.7	56965	11915	0.102	97.7
1.98-2.28	5	0.083	7.7	53567	10609	0.083	97.8
2.28-2.8	5.6	0.071	8.8	51170	9105	0.071	98.2
2.8-3.95	7.1	0.053	11.3	51136	7245	0.053	99.5

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
PHENIX	1.8_1069	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2IL3

2il3

Resolution: 1.25→30.104 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8451 / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 22.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2278	5870	5.04 %	RANDOM
R_work	0.1999	-	-	-
all	0.2013	116521	-	-
obs	0.2013	116521	95.89 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 62.01 Å² / B_iso mean: 14.1348 Å² / B_iso min: 2.45 Å²

Refinement step

Cycle: LAST / Resolution: 1.25→30.104 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3461	0	40	670	4171

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3651
X-RAY DIFFRACTION	f_angle_d	1.407	4968
X-RAY DIFFRACTION	f_chiral_restr	0.09	561
X-RAY DIFFRACTION	f_plane_restr	0.008	637
X-RAY DIFFRACTION	f_dihedral_angle_d	15.399	1380

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.25-1.2642	0.3383	196	0.3121	3403	3599	89
1.2642-1.2791	0.333	187	0.307	3382	3569	91
1.2791-1.2947	0.3093	190	0.3064	3514	3704	92
1.2947-1.3111	0.3101	200	0.2847	3500	3700	93
1.3111-1.3283	0.2883	178	0.268	3555	3733	93
1.3283-1.3465	0.2771	182	0.2574	3527	3709	94
1.3465-1.3657	0.2539	235	0.2505	3565	3800	95
1.3657-1.3861	0.2602	212	0.2501	3553	3765	95
1.3861-1.4078	0.2834	185	0.2524	3664	3849	95
1.4078-1.4309	0.2854	184	0.245	3543	3727	95
1.4309-1.4555	0.2597	175	0.2436	3659	3834	95
1.4555-1.482	0.257	207	0.2354	3609	3816	96
1.482-1.5105	0.2581	184	0.2259	3661	3845	96
1.5105-1.5413	0.2362	200	0.2205	3718	3918	96
1.5413-1.5749	0.2572	175	0.2182	3663	3838	96
1.5749-1.6115	0.2485	190	0.209	3651	3841	97
1.6115-1.6518	0.2105	167	0.2085	3744	3911	96
1.6518-1.6964	0.2527	201	0.2117	3738	3939	97
1.6964-1.7464	0.2324	195	0.2112	3734	3929	97
1.7464-1.8027	0.2494	188	0.218	3752	3940	98
1.8027-1.8671	0.244	211	0.204	3749	3960	98
1.8671-1.9419	0.2449	196	0.1979	3751	3947	98
1.9419-2.0303	0.2306	192	0.1951	3773	3965	97
2.0303-2.1373	0.2163	200	0.1881	3740	3940	98
2.1373-2.2711	0.2021	187	0.1829	3785	3972	98
2.2711-2.4464	0.2112	202	0.182	3813	4015	97
2.4464-2.6925	0.2279	193	0.1836	3861	4054	98
2.6925-3.0817	0.2159	231	0.1814	3863	4094	99
3.0817-3.8814	0.1884	210	0.1521	4020	4230	100
3.8814-30.104	0.1595	217	0.1545	4161	4378	98

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	0.5893	-0.096	-0.06	0.8751	0.2388	0.9136	-0.0252	0.1326	0.1767	-0.0852	-0.0092	0.0091	-0.1133	0.0443	0.0196	0.0384	0.0051	-0.0092	0.0518	0.0164	0.0467	17.5776	21.8555	8.647
2	1.478	0.8231	0.7686	1.4572	0.6242	1.7562	-0.0458	0.0159	0.4151	0.0182	-0.0583	0.0489	-0.3305	0.1355	0.0713	0.1148	-0.0259	-0.0091	0.0808	0.0136	0.1387	20.2047	30.6594	13.241
3	0.8976	0.0595	0.0925	1.2468	-0.2256	0.8682	0.0128	0.0052	0.0371	-0.0457	0.0373	0.0832	-0.013	-0.0822	-0.0359	0.0289	0.0152	-0.0023	0.055	0.0051	0.0405	10.5988	14.045	17.5448
4	3.6949	2.4486	-1.4339	2.3973	-0.8989	2.0221	0.0531	-0.0906	0.2185	0.0638	-0.0329	-0.1036	-0.3674	0.2335	-0.0156	0.0719	-0.0126	-0.0009	0.1124	-0.0043	0.1148	34.5847	19.2926	18.2898
5	2.3411	1.5642	0.0604	1.6694	-0.054	0.641	0.0055	-0.1324	-0.0243	-0.0461	-0.0605	-0.0126	0.0652	0.2021	0.0412	0.0491	0.0203	-0.006	0.1133	-0.0008	0.1259	35.2285	6.465	19.1064
6	2.0982	-1.4036	-0.4303	4.6683	-0.0957	3.3726	0.0869	-0.0076	-0.6554	-0.0012	0.0966	0.2995	0.5434	-0.1574	-0.1347	0.1075	0.0002	-0.0341	0.0731	-0.0192	0.2026	15.6375	-1.4068	12.1911
7	1.8959	0.6848	-0.0254	0.6205	-0.1335	0.5257	-0.0184	-0.0454	-0.0737	-0.0807	-0.0006	-0.095	0.0058	0.1516	0.0216	0.0394	0.02	0.0006	0.0646	-0.0012	0.043	23.8746	10.5738	11.4771
8	0.6216	-0.0036	-0.0545	1.062	-0.2977	0.2944	0.0275	0.1292	-0.2826	-0.1411	0.0229	-0.1426	0.1263	0.2365	-0.0252	0.0901	0.0504	-0.0058	0.113	-0.0294	0.1034	27.4931	2.695	6.6101
9	0.4499	0.113	0.1907	0.3486	-0.1404	0.4281	0.0317	0.0559	0.0333	-0.1494	-0.1301	-0.1027	-0.049	0.2403	0.0509	-0.1022	-0.0095	-0.0229	0.2061	0.0378	0.0962	34.5146	17.1434	6.9911
10	0.9465	-0.306	-0.0693	0.8933	0.1285	0.9273	0.0845	-0.1152	-0.3405	0.023	0.0044	0.1112	0.4692	-0.1481	-0.0326	0.1628	-0.0428	-0.0303	0.0566	0.0319	0.0659	15.2224	4.4126	39.4715
11	2.5528	-0.605	-0.2066	1.4514	-0.0096	1.441	0.1636	-0.1353	-0.1976	0.2352	0.0722	-0.1196	0.706	0.1616	-0.109	0.3067	0.0756	-0.1044	0.1635	0.0029	0.1339	20.8792	-0.5525	40.0576
12	3.4825	-0.6094	-0.9154	0.8697	0.6991	1.8286	-0.0402	-0.0002	-0.4124	-0.066	0.0229	0.0125	0.3328	0.1322	-0.085	0.3866	0.2553	-0.1867	0.0465	-0.0359	0.2186	24.1911	-4.697	29.9669
13	1.2852	0.2698	0.2673	2.754	-0.4383	1.1756	0.0479	-0.026	-0.2246	0.1189	0.0639	0.2514	0.2468	-0.2746	-0.061	0.0952	-0.0344	-0.0174	0.091	0.0214	0.0576	8.2158	6.792	31.371
14	1.8322	0.1522	0.571	0.6598	0.0309	1.0301	0.0411	0.0034	0.0336	0.02	-0.0245	-0.1645	-0.0267	0.1663	-0.0108	0.0418	-0.0116	0.0006	0.0678	-0.0003	0.066	27.5159	18.9983	31.2282
15	1.396	0.553	-0.4236	1.2536	0.2461	1.1332	0.0281	-0.109	0.2467	0.025	-0.027	0.0593	-0.2303	-0.0494	-0.01	0.0738	0.0099	0.0043	0.0597	-0.0148	0.06	17.797	24.2956	39.632
16	5.2693	0.2782	-0.3299	0.5081	0.0449	0.6503	-0.0113	-0.1784	-0.0051	0.0827	-0.0046	-0.1613	-0.102	0.2295	0.0057	0.0814	-0.0174	-0.0107	0.1467	0.0051	0.0789	29.5972	13.5575	45.9263

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 24 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 56 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 105 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 106 through 125 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 126 through 146 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 147 through 158 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 159 through 173 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 174 through 197 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 198 through 222 )	A
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 24 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 25 through 43 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 44 through 56 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 57 through 89 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 90 through 145 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 146 through 197 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 198 through 219 )	B

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