PDB-4kdu: Crystal structure of a glutathione transferase family member from...

ID or keywords:

Entry

Database: PDB / ID: 4kdu

Title

Crystal structure of a glutathione transferase family member from Burkholderia graminis, target efi-507264, no gsh, ordered domains, space group P21, form(1)

Components

Glutathione S-transferase domain

Keywords

TRANSFERASE / GST / glutathione S-transferase fold / enzyme function initiative / EFI / Structural Genomics

Function / homology

Function and homology information

glutathione transferase / glutathione transferase activity
Similarity search - Function

Biological species

Burkholderia graminis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.6 Å

Authors

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

Citation

Journal: To be Published
Title: Crystal structure of a glutathione transferase family member from Burkholderia graminis, target efi-507264, no gsh, ordered domains, space group P21, form(1)
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, ...

History

Deposition	Apr 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4kdu.cif.gz	253.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4kdu.ent.gz	208.3 KB	Display	PDB format
PDBx/mmJSON format	4kdu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4kdu_validation.pdf.gz	432.3 KB	Display	wwPDB validaton report
Full document	4kdu_full_validation.pdf.gz	433.6 KB	Display
Data in XML	4kdu_validation.xml.gz	21.4 KB	Display
Data in CIF	4kdu_validation.cif.gz	32.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kd/4kdu ftp://data.pdbj.org/pub/pdb/validation_reports/kd/4kdu	HTTPS FTP

-
Related structure data

Similar structure data	4ke3-2 7k7v-d 4ke3-1 4m8h-d 5mmw-d 5mku-d 4m8e-d 4kdx-2 2p1t-d 6avs-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
Other databases	TargetTrack: EFI-507264

-
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: Glutathione S-transferase domain

B: Glutathione S-transferase domain

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

1

A: Glutathione S-transferase domain

defined by author&software
26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glutathione S-transferase domain

defined by author&software
26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.603, 56.105, 67.216
Angle α, β, γ (deg.)	90.000, 107.780, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glutathione S-transferase domain Mass: 26086.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia graminis (bacteria) / Strain: C4D1M / Gene: BgramDRAFT_2467 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1FZ96
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.52 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (1 M di-Ammonium Phosphate 0.1 M Sodium Acetate); Cryoprotection (reservoir + 20% glycerol), VAPOR DIFFUSION, ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (1 M di-Ammonium Phosphate 0.1 M Sodium Acetate); Cryoprotection (reservoir + 20% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal

Density Matthews: 2.26 Å³/Da / Density % sol: 45.52 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (1 M di-Ammonium Phosphate 0.1 M Sodium Acetate); Cryoprotection (reservoir + 20% glycerol), VAPOR DIFFUSION, ...

-
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: Apr 17, 2013 / 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: 1.6→64.004 Å / Num. all: 57253 / Num. obs: 57253 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / R_merge(I) obs: 0.083 / R_sym value: 0.083 / Net I/σ(I): 7.3

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
1.6-1.69	2.7	0.261	2.9	22297	8315	0.261	93.5
1.69-1.79	2.7	0.213	3	21498	7931	0.213	94
1.79-1.91	2.8	0.16	3.2	20804	7545	0.16	95
1.91-2.07	2.8	0.131	3.3	19807	7042	0.131	95.1
2.07-2.26	2.9	0.112	4.2	18404	6448	0.112	94.8
2.26-2.53	2.9	0.094	6.7	16918	5846	0.094	94.5
2.53-2.92	2.9	0.088	7	14928	5097	0.088	93.1
2.92-3.58	3	0.063	9.5	12635	4240	0.063	92
3.58-5.06	3	0.047	12.8	9558	3189	0.047	88.4
5.06-24.196	3	0.044	14	4829	1600	0.044	79.3

-
Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.6→24.196 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8711 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 20.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2004	2898	5.06 %	RANDOM
R_work	0.168	-	-	-
obs	0.1697	57229	93.12 %	-
all	-	57229	-	-

Solvent computation

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

Displacement parameters

B_iso max: 93.13 Å² / B_iso mean: 18.7817 Å² / B_iso min: 0.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→24.196 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3320	0	0	465	3785

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3408
X-RAY DIFFRACTION	f_angle_d	1.327	4642
X-RAY DIFFRACTION	f_chiral_restr	0.075	486
X-RAY DIFFRACTION	f_plane_restr	0.007	610
X-RAY DIFFRACTION	f_dihedral_angle_d	11.603	1238

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6262	0.2586	149	0.2031	2539	2688	94
1.6262-1.6543	0.2536	151	0.2018	2564	2715	92
1.6543-1.6843	0.2306	115	0.1891	2609	2724	94
1.6843-1.7167	0.2369	131	0.1846	2580	2711	94
1.7167-1.7518	0.2306	123	0.1798	2611	2734	94
1.7518-1.7898	0.2327	127	0.177	2603	2730	94
1.7898-1.8315	0.2359	129	0.1692	2635	2764	95
1.8315-1.8772	0.1816	132	0.1683	2632	2764	95
1.8772-1.928	0.243	143	0.2056	2601	2744	94
1.928-1.9847	0.2179	142	0.1758	2652	2794	96
1.9847-2.0487	0.194	147	0.1693	2640	2787	95
2.0487-2.1219	0.2207	139	0.1832	2609	2748	95
2.1219-2.2068	0.2079	134	0.1615	2648	2782	95
2.2068-2.3072	0.2024	128	0.1708	2608	2736	94
2.3072-2.4287	0.1934	129	0.1501	2645	2774	94
2.4287-2.5807	0.1849	158	0.1563	2578	2736	94
2.5807-2.7797	0.2035	145	0.1579	2609	2754	94
2.7797-3.0589	0.1987	142	0.1652	2549	2691	92
3.0589-3.5004	0.1787	157	0.1552	2569	2726	92
3.5004-4.4058	0.1692	150	0.1412	2488	2638	89
4.4058-24.1992	0.1916	127	0.1895	2362	2489	82

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	0.9573	-0.184	-0.1738	1.2658	-0.0671	1.3577	0.0057	0.07	0.0372	-0.1173	-0.0634	-0.1622	-0.0664	0.1749	0.0193	0.0685	-0.0044	0.0135	0.0712	0.0093	0.0684	29.592	20.6283	14.6168
2	0.7295	0.4138	0.8896	1.2739	0.202	1.1686	0.0291	-0.0681	0.0515	0.1007	-0.0553	0.189	0.0853	-0.0913	-0.001	0.0605	0.0035	0.0077	0.0576	-0.0143	0.0649	12.1685	18.6732	23.568
3	1.6392	0.1871	-0.2855	1.0869	0.5317	1.5711	-0.0886	0.1321	-0.184	-0.4882	-0.0416	-0.2755	0.2398	0.5041	-0.0537	0.3184	0.04	-0.0145	0.1628	-0.0286	0.1401	16.5484	17.0914	-3.5633
4	1.43	-0.0355	-0.8143	1.3432	1.3065	3.7283	-0.0091	0.2141	0.0489	-0.3998	0.156	0.5265	0.3013	-0.4627	0.1346	0.2151	-0.0226	-0.1286	0.0943	0.0034	0.1476	4.1353	18.8414	3.7032
5	0.8568	-0.2601	0.1465	1.0294	0.1868	1.0599	-0.0277	0.0717	0.1614	-0.2044	-0.013	0.2498	-0.1162	-0.0868	0.0638	0.1061	0.0084	-0.0489	0.0697	0.0094	0.1154	10.6479	29.3651	10.7299
6	1.9812	-0.2015	0.5498	1.5563	-0.3151	1.0149	0.1179	-0.0841	-0.2129	-0.0395	-0.0254	0.1859	0.1712	-0.154	0.008	0.0927	-0.0104	-0.0258	0.0449	-0.0117	0.1128	6.5427	-1.6588	21.5499
7	1.4836	-0.319	1.8436	0.1625	-0.188	2.7076	0.2842	-0.168	-0.5147	-0.3368	0.0377	0.3363	0.3576	-0.4128	0.0071	0.2141	-0.06	-0.0814	0.2132	0.0222	0.2229	-2.453	-1.2271	18.6628
8	0.4067	0.201	0.6377	1.2061	0.1939	1.4384	0.0281	-0.1685	0.009	-0.1745	-0.0697	0.3451	-0.0388	-0.2647	0.0385	0.0526	-0.0188	-0.0213	0.1454	0.0005	0.1485	-0.7723	8.9839	18.7049
9	1.0503	0.0994	0.8366	0.8641	-0.1301	1.308	-0.021	-0.1037	-0.0237	0.0476	0.077	0.041	-0.0544	-0.1056	-0.0319	0.0684	0.0006	0.0053	0.0685	-0.002	0.0485	14.0485	7.1567	29.0812
10	0.8973	-0.2235	-0.4645	1.8475	0.8078	3.0222	0.04	-0.0173	0.0069	0.0864	-0.0101	-0.0957	0.1169	0.1712	0.0222	0.0849	0.0109	-0.008	0.0503	0.0085	0.0819	23.4182	9.0445	20.7422
11	1.5732	-0.2114	-0.3061	0.6475	-0.1336	1.986	0.1254	0.5044	0.0456	-0.2274	-0.0502	0.0462	-0.0685	-0.0548	-0.0014	0.1578	0.0736	-0.0067	0.1569	0.0052	0.0809	19.7478	-0.9388	3.546
12	0.908	0.2337	-0.2022	0.7262	-0.0726	0.8152	0.0315	0.0472	-0.1288	-0.07	-0.0418	-0.0051	0.2493	0.0898	0.0104	0.1086	0.0379	-0.0125	0.0388	-0.0021	0.0723	23.5454	-5.8136	16.5119
13	1.6726	0.1939	1.869	0.9129	0.1612	2.094	0.0516	0.0131	0.008	-0.122	-0.1333	0.15	0.2455	-0.0045	0.0461	0.1938	-0.0028	-0.0143	0.0828	-0.0156	0.0955	14.0583	-10.3942	20.8473

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 76 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 102 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 124 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 149 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 150 through 207 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 22 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 23 through 41 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 42 through 65 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 66 through 86 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 87 through 102 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 103 through 149 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 150 through 194 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 195 through 207 )	B

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi