PDB-4mdc: Crystal structure of glutathione S-transferase from Sinorhizobium...

ID or keywords:

Entry

Database: PDB / ID: 4mdc

Title

Crystal structure of glutathione S-transferase from Sinorhizobium meliloti 1021, NYSGRC target 021389

Components

Putative glutathione S-transferase

Keywords

TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / glutathione S-transferase / glutathione

Function / homology

Function and homology information

glutathione transferase / glutathione transferase activity
Similarity search - Function

Biological species

Sinorhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.78 Å

Authors

Shabalin, I.G. / Bacal, P. / Cooper, D.R. / Stead, M. / Ahmed, M. / Hammonds, J. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Citation

Journal: To be Published
Title: Crystal structure of glutathione S-transferase from Sinorhizobium meliloti 1021
Authors: Shabalin, I.G. / Bacal, P. / Cooper, D.R. / Stead, M. / Ahmed, M. / Hammonds, J. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.

History

Deposition	Aug 22, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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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PDBx/mmCIF format	4mdc.cif.gz	405.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4mdc.ent.gz	345.2 KB	Display	PDB format
PDBx/mmJSON format	4mdc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4mdc_validation.pdf.gz	469.1 KB	Display	wwPDB validaton report
Full document	4mdc_full_validation.pdf.gz	476.9 KB	Display
Data in XML	4mdc_validation.xml.gz	44.3 KB	Display
Data in CIF	4mdc_validation.cif.gz	66.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/md/4mdc ftp://data.pdbj.org/pub/pdb/validation_reports/md/4mdc	HTTPS FTP

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Related structure data

Similar structure data	6pnt-d 4k8v-3 4tyv-2 2xj9-d 5m8q-1 4ni0-1 5vdo-2 4top-d 4isj-2 4chs-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: NYSGRC-021389

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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 (9)

Deposited unit

A: Putative glutathione S-transferase

B: Putative glutathione S-transferase

C: Putative glutathione S-transferase

D: Putative glutathione S-transferase

hetero molecules

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

1

A: Putative glutathione S-transferase

B: Putative glutathione S-transferase

hetero molecules

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

2

C: Putative glutathione S-transferase

D: Putative glutathione S-transferase

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

Unit cell

Length a, b, c (Å)	182.181, 53.508, 111.123
Angle α, β, γ (deg.)	90.000, 115.880, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-570- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	0 - 229
2	1	B	0 - 229
1	2	A	0 - 229
2	2	C	0 - 229
1	3	A	0 - 229
2	3	D	0 - 229
1	4	B	-2 - 230
2	4	C	-2 - 230
1	5	B	-2 - 230
2	5	D	-2 - 230
1	6	C	-2 - 230
2	6	D	-2 - 230

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Putative glutathione S-transferase Mass: 29479.111 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: gst4, R00327, SMc00407 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q92SP3, glutathione transferase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.07 Å³/Da / Density % sol: 40.47 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 ul of 12.6 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 0.2 ul of The Cryos Suite condition #80 (8.5% PEG 1000; 8.5% ...Details: 0.2 ul of 12.6 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 0.2 ul of The Cryos Suite condition #80 (8.5% PEG 1000; 8.5% PEG 8000; 15% glycerol) and equilibrated against 1.9 M NaCl in QIAGEN EasyXtal 15-Well Tool plate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 2.07 Å³/Da / Density % sol: 40.47 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 12.6 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 0.2 ul of The Cryos Suite condition #80 (8.5% PEG 1000; 8.5% ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2013 / Details: BE-LENSES

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.78→50 Å / Num. all: 93260 / Num. obs: 93167 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / B_iso Wilson estimate: 24 Å² / R_merge(I) obs: 0.075 / Χ²: 1.874 / Net I/σ(I): 10.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	R_sym value	Χ²	% possible all
1.78-1.81	5.2	0.721	2.1	4595	0.721	0.801	100
1.81-1.84	5.2	0.595		4662		0.801	100
1.84-1.88	5.2	0.512		4582		0.867	100
1.88-1.92	5.3	0.426		4654		0.878	100
1.92-1.96	5.2	0.344		4643		0.945	100
1.96-2	5.3	0.276		4629		0.988	100
2-2.05	5.3	0.225		4621		1.039	100
2.05-2.11	5.2	0.192		4638		1.154	100
2.11-2.17	5.3	0.165		4638		1.276	100
2.17-2.24	5.3	0.151		4659		1.411	100
2.24-2.32	5.3	0.133		4665		1.544	100
2.32-2.42	5.3	0.112		4621		1.585	100
2.42-2.53	5.3	0.099		4646		1.764	100
2.53-2.66	5.3	0.086		4671		1.933	100
2.66-2.83	5.3	0.081		4664		2.211	99.9
2.83-3.04	5.2	0.071		4641		2.537	100
3.04-3.35	5.2	0.062		4708		3.206	100
3.35-3.83	5.2	0.048		4699		3.371	99.8
3.83-4.83	5.1	0.042		4730		3.66	100
4.83-50	4.9	0.047		4801		5.663	99.2

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
SHELX		phasing
DM		phasing
REFMAC	5.7.0029	refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
MLPHARE		phasing
SOLVE		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.78→29.8 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.962 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.315 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.108
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1904	4636	5 %	RANDOM
R_work	0.1614	-	-	-
obs	0.1629	92699	99.91 %	-
all	-	92782	-	-

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 max: 125.65 Å² / B_iso mean: 30.2278 Å² / B_iso min: 11.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.02 Å²	-0 Å²	-2.07 Å²
2-	-	-0.44 Å²	0 Å²
3-	-	-	2.36 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→29.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7512	0	18	904	8434

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	7894
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.02	7487
X-RAY DIFFRACTION	r_angle_refined_deg	1.68	1.983	10745
X-RAY DIFFRACTION	r_angle_other_deg	1.536	3	17206
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.643	5	976
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.598	21.865	370
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.189	15	1258
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.221	15	95
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	1158
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	8892
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	1895

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	13645	0.14
1	2	B	13645	0.14
2	1	A	13469	0.14
2	2	C	13469	0.14
3	1	A	13964	0.11
3	2	D	13964	0.11
4	1	B	13642	0.13
4	2	C	13642	0.13
5	1	B	13594	0.14
5	2	D	13594	0.14
6	1	C	13521	0.13
6	2	D	13521	0.13

LS refinement shell

Resolution: 1.78→1.826 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.306	332	-
R_work	0.276	6462	-
all	-	6794	-
obs	-	-	99.96 %

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	3.3443	0.4033	1.225	1.3378	-0.1993	1.9189	-0.0894	-0.2009	-0.0027	0.1781	0.0281	0.1488	-0.06	-0.1986	0.0612	0.1459	0.0292	0.1124	0.2126	-0.0091	0.0954	-10.504	3.266	57.244
2	1.2956	-0.871	-0.237	0.655	-0.0224	0.9511	-0.0081	0.1394	-0.2996	-0.0046	-0.1497	0.1909	0.1383	-0.0809	0.1578	0.1272	0.0063	0.0785	0.181	-0.0297	0.1162	-3.581	-9.98	47.659
3	1.9568	-0.0946	0.7463	1.4468	-0.1759	2.003	0.0134	-0.0331	-0.3271	0.267	-0.0321	0.0078	0.3644	0.0689	0.0186	0.1959	0.0403	0.0856	0.1613	0.0435	0.122	2.988	-13.507	58.095
4	4.6152	1.1847	1.0662	2.2748	0.4326	3.7224	-0.1381	-0.4706	-0.5135	0.4234	0.0288	0.0449	0.6664	-0.4448	0.1093	0.3503	-0.0556	0.1869	0.2706	0.0834	0.1865	-7.08	-16.443	63.902
5	1.7813	-0.4156	0.9427	0.1256	-0.3356	1.1487	0.0926	-0.0353	-0.0694	-0.0402	-0.0031	0.006	0.0189	0.0392	-0.0894	0.0771	-0.0026	0.0567	0.1414	0.0172	0.0568	16.991	4.391	42.163
6	0.6504	0.0922	-0.2945	0.976	-0.1844	0.691	-0.0085	-0.1173	0.0285	0.0878	-0.0142	-0.0309	-0.0625	0.0254	0.0227	0.0762	0.0055	0.0372	0.1292	-0.0036	0.035	5.827	11.611	49.769
7	1.9902	-0.4299	0.0533	2.0299	0.2525	1.4423	0.0535	0.0651	-0.2639	-0.0846	0.039	0.0302	0.1373	-0.0882	-0.0926	0.0701	-0.0065	0.0081	0.0648	-0.0014	0.0503	0.325	3.726	30.809
8	1.7795	-0.1038	0.1498	1.1366	-0.1361	1.123	0.0072	0.0755	0.0752	-0.1141	-0.0209	0.0094	-0.0707	0.0796	0.0138	0.0713	-0.0059	0.0346	0.0868	0.0177	0.0313	6.428	15.497	30.071
9	1.5173	-0.4609	-0.4099	0.782	0.0603	0.8549	0.1	-0.1013	-0.0844	0.1291	-0.08	-0.0276	0.0319	-0.0238	-0.02	0.1265	-0.0098	0.0328	0.1357	-0.0009	0.0771	38.91	15.075	6.364
10	0.7177	0.2151	0.1157	2.7083	0.9163	1.1638	0.0059	0.0935	-0.0741	-0.037	-0.0635	-0.075	0.0041	0.1274	0.0577	0.0527	0.0085	0.0405	0.0943	0.0046	0.0469	40.143	17.739	-2.076
11	1.1043	-0.3546	-0.756	0.6556	-0.0469	1.4944	0.0242	-0.0206	0.0521	0.0858	0.0242	0.0363	-0.0881	-0.1473	-0.0484	0.0737	0.0199	0.0472	0.0933	-0.0231	0.0472	20.622	15.768	4.707
12	1.5781	0.2042	-0.4843	0.6731	0.1134	2.6876	-0.0232	-0.114	-0.1841	0.0881	-0.024	0.0755	0.1026	-0.0712	0.0472	0.0683	-0.001	0.055	0.0435	0.003	0.0707	25.528	4.552	9.823
13	2.4645	-0.1303	0.8122	1.7851	0.0755	1.0353	-0.0539	0.0475	0.0603	-0.0383	0.0671	0.0627	0.0737	-0.0506	-0.0131	0.0671	0.0048	-0.0022	0.0633	-0.0166	0.0197	17.217	18.86	-18.995
14	1.6652	-0.3962	0.0277	1.9815	-0.0179	0.9826	-0.0028	0.1242	0.0618	-0.1643	-0.0898	-0.0422	0.0123	0.0858	0.0925	0.0755	0.012	0.0378	0.0979	-0.0074	0.0379	32.453	24.522	-14.2
15	1.3873	0.4681	-0.2498	1.8267	0.5312	1.4004	0.0359	0.0576	0.188	0.075	-0.1442	0.2113	-0.0479	-0.144	0.1084	0.0188	0.002	0.0123	0.0649	-0.0344	0.0628	22.308	37.412	-9.15
16	1.5573	0.8474	-0.1771	1.844	-0.0287	1.809	-0.062	0.1469	0.2321	-0.374	-0.0013	0.2488	-0.2297	-0.019	0.0634	0.1234	0.0113	-0.0422	0.0613	-0.0015	0.0598	24.587	38.004	-21.786

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 87
2	X-RAY DIFFRACTION	2	A	88 - 140
3	X-RAY DIFFRACTION	3	A	141 - 190
4	X-RAY DIFFRACTION	4	A	191 - 230
5	X-RAY DIFFRACTION	5	B	-2 - 53
6	X-RAY DIFFRACTION	6	B	54 - 109
7	X-RAY DIFFRACTION	7	B	110 - 166
8	X-RAY DIFFRACTION	8	B	167 - 230
9	X-RAY DIFFRACTION	9	C	-2 - 37
10	X-RAY DIFFRACTION	10	C	38 - 82
11	X-RAY DIFFRACTION	11	C	83 - 158
12	X-RAY DIFFRACTION	12	C	159 - 230
13	X-RAY DIFFRACTION	13	D	-2 - 75
14	X-RAY DIFFRACTION	14	D	76 - 114
15	X-RAY DIFFRACTION	15	D	115 - 166
16	X-RAY DIFFRACTION	16	D	167 - 230

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