PDB-3m1g: The structure of a putative glutathione S-transferase from Coryne...

ID or keywords:

Entry

Database: PDB / ID: 3m1g

Title

The structure of a putative glutathione S-transferase from Corynebacterium glutamicum

Components

Putative glutathione S-transferase

Keywords

TRANSFERASE / ECM4-like subfamily / GST_C family /

Structural Genomics / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

glutathione transferase activity
Similarity search - Function

Biological species

Corynebacterium glutamicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Cuff, M.E. / Marshall, N. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of a putative glutathione S-transferase from Corynebacterium glutamicum
Authors: Cuff, M.E. / Marshall, N. / Cobb, G. / Joachimiak, A.

History

Deposition	Mar 4, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 14, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3m1g.cif.gz	208 KB	Display	PDBx/mmCIF format
PDB format	pdb3m1g.ent.gz	171 KB	Display	PDB format
PDBx/mmJSON format	3m1g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m1/3m1g ftp://data.pdbj.org/pub/pdb/validation_reports/m1/3m1g	HTTPS FTP

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Related structure data

Similar structure data	1zyc-2 1zxe-2 6yxf-d 1m7u-d 4riy-2 1zyd-d 6tii-2 4z1h-d 6al2-1 1zy5-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	TargetDB: apc61549

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (5) #255 - Mar 2021 Cisplatin and DNA similarity (5)

Deposited unit

A: Putative glutathione S-transferase

B: Putative glutathione S-transferase

C: Putative glutathione S-transferase

hetero molecules

125 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative glutathione S-transferase

hetero molecules

A: Putative glutathione S-transferase

hetero molecules

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

2

B: Putative glutathione S-transferase

C: Putative glutathione S-transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	167.245, 167.245, 226.855
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	97
Space group name H-M	I422

#1: Protein	Putative glutathione S-transferase / Mass: 41176.180 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 / Gene: cg1426, Cgl1264 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21 / References: UniProt: Q8NR03, glutathione transferase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 859 / 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: 3.21 Å³/Da / Density % sol: 61.69 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2M sodium potassium tartrate, 20% PEG 3350, trypsin in situ, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97948, 0.97935

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2010

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97948	1
2	0.97935	1

Reflection

Redundancy: 11 % / Av σ(I) over netI: 36.2 / Number: 1019242 / R_merge(I) obs: 0.079 / Χ²: 1.19 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 92656 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.7	50	97.9	1	0.047	2.71	10.3
4.52	5.7	100	1	0.049	2.192	10.6
3.95	4.52	100	1	0.057	2.628	10.8
3.59	3.95	100	1	0.058	2.107	10.9
3.33	3.59	100	1	0.06	1.599	11
3.14	3.33	100	1	0.068	1.335	11.1
2.98	3.14	100	1	0.081	1.175	11.1
2.85	2.98	100	1	0.092	1.083	11.1
2.74	2.85	100	1	0.113	0.971	11.1
2.65	2.74	100	1	0.131	0.911	11.1
2.56	2.65	100	1	0.154	0.821	11.1
2.49	2.56	100	1	0.179	0.796	11.1
2.42	2.49	100	1	0.208	0.767	11.1
2.37	2.42	100	1	0.251	0.738	11.1
2.31	2.37	100	1	0.288	0.709	11.1
2.26	2.31	100	1	0.326	0.705	11.1
2.22	2.26	100	1	0.43	0.702	11.1
2.18	2.22	100	1	0.496	0.666	11.1
2.14	2.18	100	1	0.591	0.651	11.1
2.1	2.14	100	1	0.667	0.639	11.1

Reflection

Resolution: 2.1→50 Å / Num. all: 92656 / Num. obs: 92656 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / B_iso Wilson estimate: 53.5 Å² / R_merge(I) obs: 0.079 / Χ²: 1.19 / Net I/σ(I): 8.4

Reflection shell

Resolution: 2.1→2.14 Å / Redundancy: 11.1 % / R_merge(I) obs: 0.667 / Num. unique all: 4558 / Χ²: 0.639 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.1 Å / D res low: 50 Å / FOM : 0.254 / FOM acentric: 0.266 / FOM centric: 0.112 / Reflection: 92460 / Reflection acentric: 85582 / Reflection centric: 6878

Phasing MAD set

Highest resolution: 2.1 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	2.74	1	0.1	0	0	0	85582	6878
2	0.99	0.97	50.3	66.3	0.25	0.21	61095	5493

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	12.98-50	2.6	1	0.4	0.1	0	0	281	118
1	7.46-12.98	1.4	1	0.2	0.1	0	0	1422	343
1	5.23-7.46	2.09	1	0.2	0.1	0	0	3476	563
1	4.03-5.23	1.51	1	0.2	0.1	0	0	6473	775
1	3.28-4.03	1.75	1	0.1	0.1	0	0	10345	958
1	2.76-3.28	2.98	1	0.1	0	0	0	15159	1179
1	2.39-2.76	4.98	1	0.1	0	0	0	20898	1371
1	2.1-2.39	7.53	1	0.1	0	0	0	27528	1571
2	12.98-50	0.96	0.97	69.6	81.6	0.64	0.47	280	117
2	7.46-12.98	0.98	0.95	70.5	84.9	0.42	0.33	1422	343
2	5.23-7.46	0.97	0.93	54.7	67.1	0.45	0.34	3476	563
2	4.03-5.23	0.98	0.96	68.2	83.5	0.29	0.23	6472	774
2	3.28-4.03	0.99	0.98	62.9	75.3	0.25	0.19	10345	958
2	2.76-3.28	0.99	0.98	45.3	57.7	0.24	0.17	15158	1179
2	2.39-2.76	0.99	0.99	40.8	52.7	0.18	0.13	20895	1371
2	2.1-2.39	0.99	1	42.6	55.6	0.14	0.1	3047	188

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	24.5243	0.478	0.183	0.205	1.872	0
2	56.2892	0.269	0.166	0.022	2.036	0
3	34.6234	0.622	0.206	0.165	1.854	0
4	40.0523	0.29	0.175	0.026	1.8	0
5	40.0365	0.715	0.283	0.205	1.649	0
6	37.9445	0.656	0.184	0.178	1.517	0
7	36.8845	0.774	0.366	0.166	1.492	0
8	56.4128	0.31	0.164	0.01	1.758	0
9	51.9753	0.301	0.051	-0.018	1.585	0
10	49.9609	0.472	0.16	0.209	1.731	0
11	42.7874	0.633	0.186	0.162	1.527	0
12	36.7816	0.452	0.153	0.193	1.56	0
13	24.0162	0.478	0.183	0.205	2.21	0.086
14	48.4987	0.269	0.166	0.022	2.404	0.085
15	33.9884	0.622	0.205	0.166	2.224	0.083
16	52.8853	0.291	0.175	0.026	2.373	0.058
17	37.4136	0.715	0.282	0.205	1.941	0.05
18	34.5775	0.656	0.184	0.179	1.85	0.057
19	38.4265	0.774	0.366	0.166	1.916	0.048
20	53.4973	0.31	0.164	0.01	2.117	0.041
21	56.3829	0.301	0.052	-0.018	1.998	0.05
22	41.3497	0.472	0.159	0.209	2.299	0.062
23	51.8615	0.634	0.185	0.162	2.103	0.052
24	25.4904	0.452	0.152	0.193	1.717	0.045

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.98-50	0.514	0.635	0.228	399	281	118
7.46-12.98	0.524	0.596	0.226	1765	1422	343
5.23-7.46	0.549	0.597	0.252	4039	3476	563
4.03-5.23	0.454	0.487	0.182	7248	6473	775
3.28-4.03	0.406	0.431	0.14	11303	10345	958
2.76-3.28	0.337	0.354	0.121	16338	15159	1179
2.39-2.76	0.201	0.209	0.073	22269	20898	1371
2.1-2.39	0.078	0.082	0.005	29099	27528	1571

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 92460

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
11.38-100	67.3	0.755	600
8.05-11.38	64.3	0.88	1126
6.57-8.05	61.2	0.906	1434
5.69-6.57	60.7	0.874	1698
5.09-5.69	60.9	0.89	1886
4.65-5.09	62.5	0.881	2089
4.3-4.65	65.7	0.863	2250
4.02-4.3	66.9	0.846	2426
3.79-4.02	68.4	0.838	2547
3.6-3.79	67.5	0.834	2721
3.43-3.6	68.3	0.824	2841
3.29-3.43	67.5	0.791	2959
3.16-3.29	68.8	0.791	3081
3.04-3.16	68.8	0.77	3211
2.94-3.04	72.5	0.742	3307
2.85-2.94	72.8	0.741	3427
2.76-2.85	72.9	0.728	3522
2.68-2.76	75.2	0.704	3603
2.61-2.68	74.8	0.721	3745
2.55-2.61	76.3	0.686	3824
2.48-2.55	77.6	0.692	3918
2.43-2.48	79.8	0.699	4010
2.37-2.43	80.1	0.679	4091
2.32-2.37	80.3	0.683	4201
2.28-2.32	80.8	0.688	4268
2.23-2.28	84.9	0.674	4357
2.19-2.23	84.5	0.672	4428
2.15-2.19	86.1	0.681	4506
2.1-2.15	86.3	0.631	6384

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.1→45.45 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.962 / WR_factor R_free: 0.173 / WR_factor R_work: 0.148 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.925 / SU B: 5.707 / SU ML: 0.069 / SU R Cruickshank DPI: 0.123 / SU R_free: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.114
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.176	4633	5 %	RANDOM
R_work	0.151	-	-	-
all	0.152	92656	-	-
obs	0.152	92656	99.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 92.66 Å² / B_iso mean: 26.273 Å² / B_iso min: 8.52 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	0 Å²
2-	-	-0.26 Å²	0 Å²
3-	-	-	0.51 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→45.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7122	0	76	859	8057

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	7483
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5161
X-RAY DIFFRACTION	r_angle_refined_deg	1.448	1.956	10196
X-RAY DIFFRACTION	r_angle_other_deg	0.943	3	12490
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.899	5	913
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.837	23.226	372
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.449	15	1158
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.437	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1080
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	8355
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1578
X-RAY DIFFRACTION	r_mcbond_it	0.778	1.5	4491
X-RAY DIFFRACTION	r_mcbond_other	0.204	1.5	1797
X-RAY DIFFRACTION	r_mcangle_it	1.417	2	7301
X-RAY DIFFRACTION	r_scbond_it	2.195	3	2992
X-RAY DIFFRACTION	r_scangle_it	3.492	4.5	2882

LS refinement shell

Resolution: 2.103→2.158 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.247	336	-
R_work	0.2	6388	-
all	-	6724	-
obs	-	-	99.32 %

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	0.3987	-0.6714	-0.3137	2.9373	1.2785	1.0461	0.0676	0.0174	0.0143	0.0577	-0.1684	-0.0137	0.0374	-0.1397	0.1008	0.0415	-0.006	-0.0088	0.0247	-0.0241	0.0454	41.2796	20.0127	10.6453
2	1.7781	-0.3204	0.5875	0.45	0.0342	1.2279	-0.075	-0.1083	0.0927	-0.0308	-0.0306	-0.0248	-0.1587	0.2066	0.1056	0.052	-0.0526	0.0267	0.1151	-0.0237	0.0689	75.3988	38.1716	52.233
3	0.9546	-0.8635	0.2322	1.2568	-0.3514	0.4728	0.0485	0.1529	0.1286	-0.0952	-0.1261	-0.153	-0.2267	0.003	0.0776	0.2693	0.0608	-0.04	0.1133	-0.0719	0.1158	42.897	61.3977	31.6979

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 358
2	X-RAY DIFFRACTION	2	B	26 - 358
3	X-RAY DIFFRACTION	3	C	26 - 359

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