PDB-7c10: Dithiol cGrx1

ID or keywords:

Entry

Database: PDB / ID: 7c10

Title

Dithiol cGrx1

Components

Glutaredoxin

Keywords

OXIDOREDUCTASE / glutaredoxin-1 / Grx1 / domain-swapping

Function / homology

Function and homology information

cell redox homeostasis / electron transfer activity
Similarity search - Function

Biological species

Alkaliphilus oremlandii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.806 Å

Authors

Lee, K. / Hwang, K.Y.

Funding support

Korea, Republic Of, 2items

Citation

Journal: Iucrj / Year: 2020
Title: Monothiol and dithiol glutaredoxin-1 from clostridium oremlandii: identification of domain-swapped structures by NMR, X-ray crystallography and HDX mass spectrometry.
Authors: Lee, K. / Yeo, K.J. / Choi, S.H. / Lee, E.H. / Kim, B.K. / Kim, S. / Cheong, H.-K. / Lee, W.-K. / Kim, H.-Y. / Hwang, E. / Woo, J.R. / Lee, S.-J. / Hwang, K.Y.

History

Deposition	May 2, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7c10_validation.pdf.gz	452.7 KB	Display	wwPDB validaton report
Full document	7c10_full_validation.pdf.gz	454.2 KB	Display
Data in XML	7c10_validation.xml.gz	13.6 KB	Display
Data in CIF	7c10_validation.cif.gz	18.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c1/7c10 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/7c10	HTTPS FTP

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Related structure data

Related structure data	7c12C 7c13C 4tr1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2jpc-d 3n4z-2 2kap-d 6fdd-6 1dtj-1 6m3n-d 3hix-3 2b8i-d 6osn-d 2n2w-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) 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

7c12C

7c13C

4tr1S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glutaredoxin

B: Glutaredoxin

C: Glutaredoxin

D: Glutaredoxin

E: Glutaredoxin

48.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutaredoxin

defined by author
Evidence: gel filtration
9.69 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glutaredoxin

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

3

C: Glutaredoxin

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

4

D: Glutaredoxin

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

5

E: Glutaredoxin

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

Unit cell

Length a, b, c (Å)	93.420, 61.105, 93.940
Angle α, β, γ (deg.)	90.000, 104.240, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Glutaredoxin Mass: 9686.062 Da / Num. of mol.: 5 / Mutation: U13C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkaliphilus oremlandii (strain OhILAs) (bacteria) Strain: OhILAs / Gene: Clos_2129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8MIN3
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium phosphate/citric acid pH4.2, 0.2M Lithium sulfate, 20% PEG 1000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 5C (4A) / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 3, 2018

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.8→50 Å / Num. obs: 12448 / % possible obs: 98.1 % / Redundancy: 5.7 % / R_merge(I) obs: 0.047 / R_pim(I) all: 0.02 / R_rim(I) all: 0.051 / Χ²: 2.84 / Net I/σ(I): 33.7 / Num. measured all: 71066

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.8-2.85	4.2	0.126	580	0.985	0.064	0.142	1.918	95.1
2.85-2.9	4.5	0.112	634	0.989	0.055	0.125	2.015	96.4
2.9-2.96	4.7	0.107	596	0.992	0.051	0.119	2.009	97.4
2.96-3.02	4.8	0.099	610	0.993	0.046	0.109	2.151	97.3
3.02-3.08	5.1	0.094	636	0.994	0.043	0.103	2.445	98.3
3.08-3.15	5.4	0.08	573	0.996	0.036	0.088	2.489	97.6
3.15-3.23	5.4	0.075	644	0.995	0.034	0.083	2.469	99.1
3.23-3.32	5.7	0.068	628	0.997	0.029	0.074	2.658	98.9
3.32-3.42	5.8	0.067	618	0.998	0.029	0.073	2.794	99
3.42-3.53	5.9	0.06	626	0.997	0.026	0.066	3.101	98.7
3.53-3.65	6	0.057	626	0.998	0.025	0.063	3.209	99.5
3.65-3.8	6.1	0.058	632	0.997	0.025	0.063	3.525	98.4
3.8-3.97	6	0.051	641	0.998	0.022	0.056	3.458	99.5
3.97-4.18	6.1	0.049	605	0.996	0.021	0.054	3.561	99.7
4.18-4.44	6.3	0.047	641	0.998	0.02	0.052	3.618	99.1
4.44-4.79	6.3	0.044	628	0.997	0.019	0.048	3.446	98.9
4.79-5.27	6.3	0.038	631	0.998	0.016	0.041	2.902	99.4
5.27-6.03	6.3	0.036	643	0.999	0.015	0.039	2.707	99.4
6.03-7.59	6.9	0.034	651	0.999	0.014	0.037	2.571	99.7
7.59-50	6.3	0.03	605	0.999	0.013	0.033	2.496	90.2

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4TR1

4tr1

Resolution: 2.806→37.069 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.66 / Phase error: 28.01

	R_factor	Num. reflection	% reflection
R_free	0.2754	1245	10.01 %
R_work	0.2192	-	-
obs	0.2248	12443	97.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 164.92 Å² / B_iso mean: 67.4209 Å² / B_iso min: 23.95 Å²

Refinement step

Cycle: final / Resolution: 2.806→37.069 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2918	0	0	0	2918
Num. residues	-	-	-	-	369

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.8065-2.9188	0.3018	131	0.2718	1176	94
2.9188-3.0516	0.3487	135	0.2733	1225	98
3.0516-3.2124	0.2911	140	0.2557	1245	98
3.2124-3.4135	0.2633	137	0.251	1238	99
3.4135-3.6768	0.2616	139	0.224	1256	99
3.6768-4.0465	0.2655	140	0.2141	1247	99
4.0465-4.631	0.256	140	0.1827	1269	99
4.631-5.8309	0.2356	142	0.1902	1276	99
5.8309-37.069	0.3187	141	0.2229	1266	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	5.3782	-4.3837	-2.1084	8.2279	-1.3528	4.1945	-0.0107	0.6467	-0.3872	-0.2792	-0.2487	0.4406	-0.3243	0.4512	0.2722	0.3355	-0.1049	-0.0561	0.5742	-0.0431	0.336	5.8265	3.4659	28.5508
2	3.1153	-3.3866	-0.1637	7.5716	-2.2599	2.124	-0.6004	-0.0969	0.7643	0.0794	-0.1359	-1.4815	-0.5732	0.8189	0.446	0.3784	0.0601	-0.0723	1.0144	0.1133	0.566	11.975	4.3189	29.1016
3	5.4257	-2.7802	-0.1916	3.7485	-0.1898	7.6944	-0.0387	0.2295	-0.7808	-0.0318	0.1697	-0.4817	0.1313	2.2402	-0.0086	0.4031	0.0578	-0.063	0.7852	0.0592	0.5511	17.263	-5.3987	37.3911
4	9.2169	0.1779	3.2596	4.8223	-5.5402	7.585	0.2925	0.2568	0.2913	-0.145	-0.4328	-0.0969	0.0022	1.0726	0.0449	0.2655	-0.0741	0.0476	0.5538	-0.0684	0.2788	8.0647	-2.2594	36.9071
5	5.0851	-4.0622	3.832	3.5323	-2.9194	3.0412	0.3717	-1.9649	-0.4312	0.89	-0.2522	0.222	0.8004	-1.2931	0.0398	0.392	-0.0224	0.057	0.7536	0.0179	0.4976	3.6435	2.494	38.9544
6	3.1563	-3.0513	3.6237	3.0298	-3.567	4.3177	0.7737	-0.4583	0.5978	0.8443	-0.0808	1.6262	-0.1798	-3.0537	-0.696	0.553	-0.0143	0.0862	0.881	-0.1482	0.6575	-2.7371	8.3684	37.3047
7	3.7052	-2.9741	-1.6228	3.8421	3.5701	6.4866	0.0214	-0.4829	-0.5065	0.5145	0.1572	-0.739	1.0538	1.0356	-0.3702	0.547	0.6169	0.1486	-0.0007	-0.387	0.4804	4.533	-22.9512	29.167
8	0.6967	0.8275	-1.7011	9.0236	-0.6586	4.9721	-0.3315	0.374	0.1864	-0.9856	0.1905	0.1392	-0.0915	-0.4101	0.2349	0.3927	0.1458	-0.0083	0.5496	-0.1471	0.4363	-3.6725	-16.4618	33.3817
9	2.072	-1.239	3.8823	7.4441	-3.2804	8.6933	0.6705	0.3239	-1.4318	-0.5888	-0.4363	-0.6262	2.1877	0.4596	-0.2008	0.6573	0.1311	-0.0109	0.5361	-0.2133	0.5669	-0.1659	-25.3866	31.8325
10	7.813	0.5815	-4.8266	4.0419	0.5228	7.5539	-0.5268	-0.5103	-1.5729	0.9698	-0.1829	-1.0844	0.8041	1.3784	0.6787	0.4323	0.3192	-0.07	0.8554	-0.0616	0.6587	14.3931	-17.293	32.7031
11	5.9913	2.3214	-3.0754	1.9847	-3.2059	9.0109	-0.0888	0.4154	-0.3661	-0.698	-0.3584	-0.5424	0.7897	-0.1381	0.1146	0.5119	0.1603	-0.0478	0.6101	-0.0889	0.4124	7.1968	-16.4087	25.8843
12	3.4425	3.1248	-1.3371	3.8116	0.1037	2.4473	0.5901	1.0643	-1.821	-1.7436	-0.52	-0.8292	-0.6413	-0.0204	0.1389	0.7541	0.0958	-0.0762	0.856	-0.0217	0.8856	2.4071	-18.676	21.33
13	2.1274	2.2479	1.3895	7.5905	-3.8771	6.5649	-0.9293	1.1665	-0.0151	-1.9852	0.4605	0.883	-1.3513	-0.7696	0.4275	0.9864	0.0162	-0.1537	0.9651	-0.1849	0.5227	-5.4765	-20.1311	18.9933
14	3.8401	-0.4035	2.7327	6.345	0.7914	2.6723	-0.1268	-0.667	0.5017	-0.4882	0.0358	0.0245	-0.5437	-0.8506	-0.0655	0.4725	0.1352	0.0226	0.4819	0.108	0.3271	-0.959	-19.3695	47.1171
15	9.7184	-1.705	3.1869	7.3107	-0.9097	7.8745	-0.0298	0.3166	0.3208	-1.1338	0.1233	0.4874	-0.0992	0.5875	-0.1694	0.337	0.0192	-0.0537	0.5044	0.0832	0.3009	1.3962	-9.9951	44.9519
16	3.471	2.5717	1.7246	5.7645	4.583	6.0957	-0.3868	0.388	-0.9176	0.0603	0.6735	-0.8561	0.4054	1.5967	-0.0966	0.6077	0.182	-0.1753	0.4474	-0.0839	0.6015	3.1628	-20.3571	45.9158
17	8.3367	5.8619	-4.0236	4.6759	-3.8283	3.9076	-0.8983	0.6938	-1.7896	-0.1648	0.5797	1.5011	1.4213	0.0963	0.0478	0.8763	0.1596	-0.0724	0.2987	-0.0044	0.8207	-5.141	-30.835	50.5673
18	5.4506	-1.3457	-2.0363	8.5917	-6.0423	7.3866	0.03	-0.604	-0.8555	-0.3999	0.2118	0.2403	1.89	0.7147	-0.2734	0.2901	0.1132	-0.0705	0.4195	-0.0638	0.4108	-5.8622	-21.585	52.3883
19	7.9837	2.6465	0.2647	4.1738	5.2312	7.9822	0.0992	-1.5688	0.2385	2.143	-0.1928	-0.677	0.6892	0.2243	-0.0556	0.3946	0.0971	-0.1822	0.8905	0.183	0.8943	-3.5371	-16.6012	56.3874
20	3.5262	3.4105	0.2602	3.6048	1.5405	5.6788	-0.2602	-2.0126	-0.1662	0.4309	0.7249	-0.224	-2.1283	-2.509	-0.3767	0.834	0.2601	0.0982	1.0057	0.2303	0.6797	-0.7854	-8.1486	57.5819
21	2.9248	-2.0809	-0.3655	8.9176	-0.419	5.0026	0.0265	0.3186	-0.0333	0.1813	-0.5689	-0.1832	0.362	0.3799	0.5237	0.4132	0.0001	-0.0332	0.9042	-0.0203	0.3524	13.0043	-0.9772	16.7605
22	9.2702	4.7092	-1.3605	7.6669	-1.7272	5.39	-0.1724	0.2726	0.385	-0.3886	0.1202	-0.4511	0.0597	1.5499	0.0569	0.423	-0.0203	-0.0357	1.1408	0.035	0.4713	15.3981	5.4365	8.1574
23	1.7597	-2.1751	0.1275	4.779	-4.9114	2.0157	1.2413	1.8872	-0.7928	-2.495	-1.2672	-0.0905	0.362	-1.3214	0.3697	0.5602	0.2701	0.4357	1.5108	-0.0848	0.4668	13.4064	-9.7578	4.3954
24	2.4666	1.3706	-2.797	4.7004	2.8949	9.1489	-0.0375	0.1556	-0.632	-0.7776	-0.2531	0.1376	-0.9476	-1.0359	0.3005	0.6288	0.124	-0.0616	0.7964	-0.0865	0.4421	-4.2074	10.3362	5.2334
25	9.2116	2.6923	2.3344	7.1186	-4.8574	5.3423	-0.8528	1.2643	1.2997	0.9451	0.561	0.348	-1.931	-1.2439	-0.1089	0.6114	0.0528	0.0466	1.0662	-0.1034	0.3994	-7.9525	16.4109	4.7709
26	8.5434	0.2918	-1.6878	2.5884	0.1523	8.2664	-0.5564	-0.9906	1.0763	-0.4083	-0.0508	-0.4356	-1.9138	1.4025	0.699	0.9705	-0.2368	-0.1579	0.7717	0.0119	0.6138	6.3481	19.7549	12.2679
27	4.2532	0.1248	2.771	4.9382	3.428	4.0383	-0.6985	0.0201	0.9318	1.8832	0.1591	-1.1404	-0.8754	0.0108	0.3311	0.72	-0.0775	-0.1763	0.5661	-0.0429	0.406	3.0141	12.3588	15.6967
28	4.5236	5.7853	-0.565	9.9501	-3.5673	3.4182	0.237	-0.2385	0.4966	1.2232	-0.3458	0.0638	-2.1118	-0.9593	0.0876	0.9898	0.1543	-0.1997	0.6933	-0.0503	0.5039	-6.8508	14.4868	16.7333
29	4.0707	-2.979	-4.1812	9.0844	-2.532	9.7806	-1.1239	-1.5928	0.6109	1.1234	0.4525	-0.1983	0.422	-1.4155	0.4745	0.7171	0.3472	0.0898	1.1266	-0.0335	1.0043	-9.6049	3.3347	12.8948
30	4.6319	-4.6185	1.8616	5.0413	-3.3898	6.5381	-1.6005	-0.5982	-0.8542	2.998	0.4318	0.7143	-0.6708	0.5925	0.8681	1.0212	-0.1358	0.0369	1.2352	-0.0107	0.6701	-14.854	9	15.3722

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 25 )	A	2 - 25
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 38 )	A	26 - 38
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 47 )	A	39 - 47
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 58 )	A	48 - 58
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 59 through 67 )	A	59 - 67
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 68 through 76 )	A	68 - 76
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 9 )	B	4 - 9
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 10 through 25 )	B	10 - 25
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 26 through 34 )	B	26 - 34
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 35 through 47 )	B	35 - 47
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 48 through 58 )	B	48 - 58
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 59 through 67 )	B	59 - 67
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 68 through 76 )	B	68 - 76
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 2 through 15 )	C	2 - 15
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 16 through 25 )	C	16 - 25
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 26 through 38 )	C	26 - 38
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 39 through 47 )	C	39 - 47
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 48 through 58 )	C	48 - 58
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 59 through 67 )	C	59 - 67
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 68 through 76 )	C	68 - 76
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 4 through 38 )	D	4 - 38
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 39 through 67 )	D	39 - 67
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 68 through 76 )	D	68 - 76
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 4 through 25 )	E	4 - 25
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 26 through 34 )	E	26 - 34
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 35 through 47 )	E	35 - 47
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 48 through 54 )	E	48 - 54
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 55 through 64 )	E	55 - 64
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 65 through 69 )	E	65 - 69
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 70 through 76 )	E	70 - 76

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