PDB-5vlm: Crystal structure of EilR in complex with crystal violet

ID or keywords:

Entry

Database: PDB / ID: 5vlm

Title

Crystal structure of EilR in complex with crystal violet

Components

Regulatory protein TetR

Keywords

TRANSCRIPTION / transcription factor

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Enterobacter lignolyticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.403 Å

Authors

Pereira, J.H. / Ruegg, T.L. / Chen, J. / Novichkov, P. / DeGiovani, A. / Tomaleri, G.P. / Singer, S. / Simmons, B. / Thelen, M. / Adams, P.D.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2018
Title: Jungle Express is a versatile repressor system for tight transcriptional control.
Authors: Ruegg, T.L. / Pereira, J.H. / Chen, J.C. / DeGiovanni, A. / Novichkov, P. / Mutalik, V.K. / Tomaleri, G.P. / Singer, S.W. / Hillson, N.J. / Simmons, B.A. / Adams, P.D. / Thelen, M.P.

History

Deposition	Apr 25, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 27, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5vlm.cif.gz	871.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5vlm.ent.gz	753.9 KB	Display	PDB format
PDBx/mmJSON format	5vlm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vl/5vlm ftp://data.pdbj.org/pub/pdb/validation_reports/vl/5vlm	HTTPS FTP

-
Related structure data

Related structure data	5vl9C 5vlgC C: citing same article (ref.)
Similar structure data	5vlg-4 5vlg-2 5vlg-1 5vlg-3 5mym-1 3aux-d 3e7q-d 5dtd-d 3jra-d 4ihw-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5vl9C

5vlgC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Regulatory protein TetR

B: Regulatory protein TetR

C: Regulatory protein TetR

D: Regulatory protein TetR

E: Regulatory protein TetR

F: Regulatory protein TetR

G: Regulatory protein TetR

H: Regulatory protein TetR

hetero molecules

177 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Regulatory protein TetR

B: Regulatory protein TetR

hetero molecules

defined by author&software
Evidence: native gel electrophoresis
44.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Regulatory protein TetR

D: Regulatory protein TetR

hetero molecules

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

3

E: Regulatory protein TetR

F: Regulatory protein TetR

hetero molecules

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

4

G: Regulatory protein TetR

H: Regulatory protein TetR

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.397, 79.229, 105.579
Angle α, β, γ (deg.)	90.00, 97.10, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Regulatory protein TetR Mass: 21709.783 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter lignolyticus (bacteria) / Gene: Entcl_2353 / Production host: Escherichia coli (E. coli) / References: UniProt: E3G817
#2: Chemical	ChemComp-CVI / CRYSTAL VIOLET Mass: 372.526 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₅H₃₀N₃ / Comment: antifungal, antibiotic*YM

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Tri-Sodium Citrate, 20 % PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Oct 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.4→50 Å / Num. obs: 20683 / % possible obs: 93.4 % / Redundancy: 2.9 % / Net I/σ(I): 3.9

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_2650: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.403→48.644 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.61

	R_factor	Num. reflection	% reflection
R_free	0.2717	2019	10.06 %
R_work	0.2049	-	-
obs	0.2115	20065	90.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.403→48.644 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12000	0	224	0	12224

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	12459
X-RAY DIFFRACTION	f_angle_d	0.491	16838
X-RAY DIFFRACTION	f_dihedral_angle_d	8.644	7316
X-RAY DIFFRACTION	f_chiral_restr	0.033	1826
X-RAY DIFFRACTION	f_plane_restr	0.002	2171

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.4028-3.4879	0.3548	120	0.28	1110	X-RAY DIFFRACTION	79
3.4879-3.5822	0.3694	131	0.2821	1149	X-RAY DIFFRACTION	81
3.5822-3.6876	0.2991	131	0.2597	1171	X-RAY DIFFRACTION	84
3.6876-3.8066	0.3464	140	0.2472	1197	X-RAY DIFFRACTION	84
3.8066-3.9425	0.3264	140	0.2483	1197	X-RAY DIFFRACTION	85
3.9425-4.1003	0.3205	135	0.2297	1235	X-RAY DIFFRACTION	87
4.1003-4.2868	0.2575	146	0.1976	1265	X-RAY DIFFRACTION	91
4.2868-4.5127	0.2692	142	0.1932	1356	X-RAY DIFFRACTION	95
4.5127-4.7952	0.213	161	0.1784	1373	X-RAY DIFFRACTION	97
4.7952-5.165	0.2327	145	0.1944	1383	X-RAY DIFFRACTION	97
5.165-5.6841	0.2991	158	0.2042	1400	X-RAY DIFFRACTION	97
5.6841-6.505	0.3139	154	0.2177	1393	X-RAY DIFFRACTION	97
6.505-8.1892	0.2485	158	0.1786	1401	X-RAY DIFFRACTION	97
8.1892-48.6486	0.1932	158	0.1447	1416	X-RAY DIFFRACTION	95

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	6.6023	0.3343	-0.5609	6.918	-6.9169	8.1827	-0.7448	-1.0776	-0.2004	0.661	0.2132	-1.1409	0.0265	0.0665	0.3418	0.614	0.039	0.02	1.0089	-0.0798	0.3451	-25.3053	8.6552	7.0378
2	4.5366	-3.6992	4.7971	5.0337	-3.7105	5.0964	0.0589	0.1153	-0.1378	0.2455	-0.2157	-0.2597	0.062	1.3705	0.2583	0.3767	0.1851	-0.042	0.7983	0.1205	0.2605	-17.1678	12.7207	2.6915
3	1.6351	0.4168	1.7686	4.881	-0.24	6.571	-0.6495	-0.4695	-0.2704	0.3168	0.4007	-0.7398	0.5689	0.7567	0.0366	0.3865	-0.0239	-0.1025	0.449	0.2489	0.5303	-27.4953	6.8948	0.1758
4	1.1755	0.4809	-0.1046	0.844	-0.4369	0.2483	0.1697	-0.4357	0.4069	0.2026	-0.4838	0.5806	-0.0118	-0.528	0.3035	1.1931	0.4563	0.5604	1.3519	-0.3014	1.0548	-51.2387	17.5174	3.3506
5	3.9964	0.3136	1.4209	2.4655	-1.5662	3.0952	0.2387	-0.2473	0.0094	-0.0013	-0.134	0.289	0.0981	-0.1652	-0.1291	0.344	-0.0491	0.0445	0.4748	-0.0937	0.2323	-42.7924	14.7475	-8.3394
6	6.9124	3.5264	0.1023	5.3672	-1.6631	3.8296	0.089	0.0176	0.7188	-0.0971	-0.3672	0.069	0.2061	0.2767	0.2357	0.2918	-0.073	0.0791	0.5034	0.0028	0.2379	-42.5114	21.916	-16.5391
7	7.5936	-0.103	-3.5488	5.5033	-3.5808	5.3892	-0.1137	-0.6053	1.0249	0.664	-0.121	0.4868	0.0879	-0.0391	-0.141	0.3713	0.014	0.1235	0.6614	-0.1001	0.4618	-51.8736	25.5544	-13.729
8	3.7366	-0.907	2.4884	5.4961	-2.1878	4.5496	-0.5096	0.4663	0.4863	-0.1111	-0.4026	-0.1233	-0.3747	0.8537	0.6096	0.4387	0.0863	-0.1211	0.9291	-0.0865	0.531	-19.9536	25.1067	-43.9089
9	2.7001	0.99	-2.7995	0.8512	-1.3901	3.1882	-0.1017	0.6462	0.0099	0.2305	-0.3725	-0.425	-0.8801	1.2736	0.1931	0.5071	-0.1649	0.071	0.8445	0.2706	0.5893	-13.3025	23.4463	-38.1878
10	3.3902	1.3667	-0.3935	7.784	-1.7948	6.8235	0.5252	0.2054	0.5033	0.2601	-0.1135	-0.3218	-0.3373	-0.593	-0.1141	0.316	0.0409	0.1514	0.3567	0.2137	0.3964	-28.7689	25.2171	-36.5626
11	0.6558	0.0918	-0.3201	0.4068	-0.0941	0.1632	-0.1226	0.3218	0.2311	-0.6634	-0.1109	0.5811	-0.5497	-0.6783	0.4169	0.8309	-0.1062	-0.4223	1.2264	0.2558	0.653	-47.7412	23.1817	-43.1088
12	6.5222	-1.6062	0.3777	3.2856	0.1816	3.4615	0.4537	0.3694	0.4942	-0.1826	-0.4106	-0.0442	-0.1715	-0.2931	-0.0737	0.2796	0.0252	0.0129	0.522	0.1012	0.1976	-40.2012	23.781	-30.9608
13	4.2131	-1.1864	-0.9288	4.4414	0.0835	3.1138	0.1134	-0.1171	-0.2663	-0.2851	-0.2784	0.1908	0.0579	-0.9736	0.1983	0.2729	-0.0904	0.064	0.4764	-0.0462	0.1991	-46.8446	16.5599	-24.3643
14	7.5436	-2.9945	2.0903	2.76	-3.167	8.342	-0.0978	0.3468	-0.1936	0.5115	-0.187	-0.2753	0.2127	0.5061	0.131	0.5175	-0.1182	-0.0254	0.5775	-0.0565	0.442	7.0223	28.2268	10.1055
15	5.5951	0.4996	1.678	1.4279	-1.2807	2.8702	0.2342	-0.1177	0.6305	0.3554	-0.1054	0.5109	-0.1903	-0.0388	-0.0824	0.3384	0.0886	0.0505	0.7326	-0.0955	0.5034	-7.2692	37.1869	-3.1254
16	4.6373	0.5237	1.0722	1.8772	-0.5373	3.3418	0.0703	0.267	1.1746	-0.0092	0.2603	0.3972	-0.3614	-0.5202	-0.3459	0.3904	0.0995	0.0784	0.3556	0.0786	0.5703	-6.6958	43.8778	-12.9436
17	7.9032	6.9727	-5.8672	7.1282	-5.1498	7.8331	-0.5702	1.1453	-1.086	-0.9263	-0.0298	-0.752	0.3143	1.1825	0.3331	0.6284	0.1601	-0.2232	1.2654	-0.1327	0.6981	21.9534	30.5755	-38.3628
18	6.8495	1.0535	-5.8585	4.2957	-2.7102	9.1147	0.3974	-0.2514	-0.7016	-0.2664	-0.9038	-0.2849	0.1552	0.671	0.4583	0.3789	0.1317	-0.1693	0.5408	-0.137	0.5249	26.0392	27.8898	-31.1106
19	5.175	-0.4145	-1.1754	6.6226	1.0727	3.2694	0.6151	0.9778	-0.4216	-0.0274	-0.1861	0.3341	-0.115	0.4139	-0.1746	0.451	0.0438	-0.0988	0.3519	-0.1661	0.2852	12.0307	35.2132	-31.4328
20	6.2881	-4.2851	-0.5794	9.61	-3.7945	6.3998	0.0962	0.6425	-0.1454	-0.3394	-0.0037	0.4449	-0.2205	-0.892	-0.1375	0.3963	0.1583	-0.1608	0.5556	-0.1116	0.4934	-8.841	39.1277	-37.0249
21	1.8997	-2.8874	-1.4691	4.6208	2.9156	3.1576	0.3492	0.4497	-0.8096	-0.0997	-0.6752	0.6547	0.2518	-0.6187	-0.2307	0.3629	0.052	-0.2547	0.5738	-0.2408	0.597	-2.7971	28.678	-31.0701
22	6.3128	-0.3491	-0.8653	4.4862	-0.3488	4.6577	0.0864	-0.0215	-0.0107	0.0238	-0.0661	0.2395	-0.2439	-0.6331	-0.028	0.2493	-0.0622	-0.0091	0.3283	-0.0472	0.2576	-2.7945	38.2549	-23.429
23	5.1942	1.2533	-0.5852	3.3326	0.0562	2.1506	-0.2209	-0.1229	-0.0672	0.1682	0.2578	-0.7567	0.0934	-0.253	-0.0286	0.3417	0.0519	0.0204	0.2175	0.0028	0.3443	-42.9202	68.7226	-12.3649
24	1.6524	0.1983	0.5463	3.6974	-0.5931	1.9599	-0.1369	-0.4006	0.1091	-0.7378	0.1879	0.1204	0.3292	-0.0015	-0.0058	0.3584	-0.1499	0.0415	0.5181	-0.0713	0.207	-57.9719	60.5887	-24.4817
25	4.2798	-1.1965	0.1939	1.8807	1.4109	1.3985	0.1179	0.4154	0.967	-2.0006	-0.5185	-1.4165	0.7456	0.1426	0.4323	1.1182	0.0823	0.4264	1.4592	-0.0104	0.6835	-36.1836	73.5263	-59.7118
26	7.6173	2.1445	-4.348	7.945	-4.4942	4.0054	-0.2395	1.2813	0.5205	0.4237	0.3558	-1.3541	-1.9948	-1.0922	-0.1652	1.0105	-0.0089	0.0921	0.9317	-0.0331	0.756	-30.2415	76.6002	-53.1174
27	0.1968	-0.1097	0.1011	0.2998	0.3465	1.4816	0.0244	0.0323	0.003	0.0479	-0.0448	0.044	0.0531	-0.0132	-0.4266	1.0059	-0.3436	0.1737	0.5684	-0.2409	0.2775	-44.1456	70.997	-50.7177
28	8.3357	1.1266	1.3447	0.152	0.187	2.2647	-0.0165	0.1848	-0.0998	-0.9658	-0.0402	2.2798	0.8388	-0.776	-0.187	1.2612	-0.5598	-0.1329	0.984	-0.3965	1.355	-59.2281	56.6264	-55.2395
29	2.6858	0.5543	0.8035	0.4072	0.0249	2.0427	-0.2113	-0.0593	-0.2605	-0.3728	0.2368	-0.0322	0.2556	0.0377	-0.0744	0.8832	-0.2968	0.0483	0.7012	-0.1307	0.2846	-54.2385	64.2848	-44.1351
30	5.1736	1.0142	1.8169	0.9354	-0.5072	1.9075	0.3111	0.2536	-0.9565	-0.7143	-0.1315	-0.1892	0.7911	-0.5143	-0.1967	0.7592	-0.2046	0.093	0.4557	-0.1297	0.2624	-56.4656	56.7249	-35.2249
31	5.7321	3.4292	3.409	3.0699	0.1086	8.078	-0.6056	-1.2182	1.0405	0.4802	0.3211	1.7475	-0.4075	-1.2042	0.1501	0.707	0.2486	0.1389	0.9698	0.2679	0.9301	-13.8507	53.914	-43.3487
32	7.2233	1.4577	-6.7653	7.7476	-0.3267	7.7505	-0.7628	1.1432	-0.0404	-0.0583	0.5703	1.7885	-0.3802	-0.8794	0.1035	0.6256	-0.0587	-0.263	0.5759	0.2597	0.9126	-19.6492	47.7868	-52.3638
33	1.8628	-1.8759	-0.5044	3.4393	0.5447	1.4816	0.5304	-0.2156	1.1239	0.5834	0.6952	0.5329	-0.4836	-0.1055	-0.7572	1.5578	0.6637	-0.0952	0.8342	-0.1146	1.6881	-21.3929	59.5647	-48.3391
34	4.4181	3.3381	3.2694	7.9649	1.928	9.0997	0.1994	-1.2972	0.9778	0.642	0.1551	0.5614	0.0026	-1.3991	-0.3128	0.3121	-0.1527	0.0176	0.7361	-0.0068	0.6368	-5.2921	51.956	-50.0549
35	6.6062	-2.8862	-0.06	6.0214	1.4665	4.7601	-0.7905	-0.3704	0.2404	0.1004	1.0342	0.06	-0.0637	0.1383	0.1442	0.9567	0.0285	-0.1897	0.3041	-0.0006	0.321	13.6811	41.7429	-44.4717
36	2.7159	-0.2441	0.5504	2.8206	0.7524	3.4063	0.0831	-0.3361	0.251	-0.2509	0.6094	0.3511	-0.4047	0.1395	-0.3627	0.4689	-0.1559	-0.0982	0.5587	0.1645	0.628	5.5961	47.3024	-55.2161
37	6.754	2.0475	1.1412	2.0573	0.1202	3.4946	0.0859	0.1056	-0.7164	-0.2147	0.0113	-0.1499	0.0972	-0.1639	-0.1654	0.6526	-0.3087	-0.0312	0.6856	-0.0347	0.1898	8.0915	39.4942	-62.4416
38	5.5817	0.4331	4.3317	8.8554	2.9747	6.378	0.7377	0.0243	-0.9142	0.2253	0.155	0.3999	0.1668	-0.0805	-0.5984	0.5367	-0.2118	-0.0982	0.4861	-0.0085	0.3609	16.4607	35.1268	-57.5326
39	7.7191	-0.8538	2.5514	7.5618	6.3455	8.0101	0.1753	0.3467	-0.6021	-0.27	-0.869	1.9354	1.4085	-0.2807	0.4052	1.0342	0.0679	0.1299	0.658	-0.0807	0.6797	-8.1751	36.2263	-95.9397
40	4.8538	-0.7911	-0.5096	4.6355	-1.0847	3.7333	-0.3156	0.1925	-0.0187	-0.6862	0.188	0.2961	0.2665	-0.0825	0.1769	0.5417	-0.1713	0.034	0.5258	-0.0209	0.2357	-9.2054	37.7725	-88.5575
41	1.9618	2.3445	2.1853	5.2933	2.4154	3.4717	-0.035	0.5095	-0.869	-0.9145	0.521	-1.4263	0.0242	0.4252	-0.1184	0.8993	-0.3841	0.2697	0.5106	-0.2507	0.7495	19.9053	38.6446	-87.2605
42	2.8205	-2.7164	0.5463	3.6606	1.1065	5.2497	0.1647	-0.3018	-0.3625	-0.0328	0.3866	-0.3148	-0.1413	0.1222	-0.575	0.4071	-0.083	-0.0774	0.2222	0.0061	0.3927	9.5445	38.5153	-75.2469
43	7.1134	-2.0555	3.068	4.0298	-1.0916	3.618	-0.3187	-0.5433	1.495	-0.4721	0.6472	-1.0315	-0.5594	0.3899	-0.2085	0.4825	-0.2176	0.0438	0.5003	-0.2922	0.6129	17.9652	47.7142	-68.8061

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 42 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 43 through 70 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 71 through 78 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 79 through 147 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 148 through 174 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 175 through 192 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 4 through 24 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 53 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 54 through 70 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 71 through 78 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 79 through 147 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 148 through 192 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 6 through 72 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 73 through 147 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 148 through 192 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 24 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 25 through 51 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 52 through 71 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 72 through 85 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 86 through 94 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 95 through 192 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 5 through 111 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 112 through 192 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 2 through 24 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 25 through 51 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 52 through 70 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 71 through 78 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 79 through 147 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 148 through 192 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 5 through 23 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 24 through 38 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 39 through 51 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 52 through 70 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 71 through 85 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 86 through 147 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 148 through 174 )
38	X-RAY DIFFRACTION	38	chain 'G' and (resid 175 through 192 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 2 through 24 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 25 through 70 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 71 through 78 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 79 through 168 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 169 through 192 )

-
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