PDB-3wu6: Oxidized E.coli Lon Proteolytic domain

ID or keywords:

Entry

Database: PDB / ID: 3wu6

Title

Oxidized E.coli Lon Proteolytic domain

Components

Lon protease

Lon protease family

Keywords

HYDROLASE / OXIDIZED FORM /

LON PROTEASE / CATALYTIC DYAD SER-LYS /

ATP BINDING

Function / homology

Ribosomal Protein S5; domain 2 - #10 /

Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / :

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Nishii, W. / Kukimoto-Niino, M. / Terada, T. / Shirouzu, M. / Muramatsu, T. / Yokoyama, S.

Citation

Journal: Nat. Chem. Biol. / Year: 2015
Title: A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Authors: Nishii, W. / Kukimoto-Niino, M. / Terada, T. / Shirouzu, M. / Muramatsu, T. / Kojima, M. / Kihara, H. / Yokoyama, S.

History

Deposition	Apr 22, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 17, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Download

PDBx/mmCIF format	3wu6.cif.gz	427.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3wu6.ent.gz	354 KB	Display	PDB format
PDBx/mmJSON format	3wu6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wu/3wu6 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/3wu6	HTTPS FTP

-
Related structure data

Related structure data	3wu3C 3wu4C 3wu5C 1rr9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3wu5-d 3wu4-d 1rre-d 1rr9-d 3wu3-d 1pr1-1 4ttj-1 6eyp-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lon protease

B: Lon protease

C: Lon protease

D: Lon protease

E: Lon protease

F: Lon protease

hetero molecules

129 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: Lon protease

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

3

B: Lon protease

hetero molecules

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

4

C: Lon protease

hetero molecules

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

5

D: Lon protease

hetero molecules

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

6

E: Lon protease

hetero molecules

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

7

F: Lon protease

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.438, 86.438, 124.936
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Lon protease / Lon protease family Mass: 21366.500 Da / Num. of mol.: 6 Fragment: C-TERMINAL PROTEOLYTIC DOMAIN, UNP RESIDUES 585-784 Mutation: S679A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12, W3110 / Gene: LON, ECDH1_3170, ECDH1ME8569_0424 / Plasmid: PMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9QQ79, endopeptidase La
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.1 Å³/Da / Density % sol: 41.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.1M AMMONIUM SULFATE, 0.1M PIPES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 96667 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / R_sym value: 0.07 / Net I/σ(I): 23.2
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.8 / R_sym value: 0.88 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX		model building
PHENIX	(PHENIX.REFINE: 1.8.1_1168)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RR9

1rr9

Resolution: 1.8→32.11 Å / SU ML: 0.22 / σ(F): 1.96 / Phase error: 26.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.226	4818	4.99 %
R_work	0.189	-	-
obs	0.191	96608	99.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→32.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8277	0	25	302	8604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8449
X-RAY DIFFRACTION	f_angle_d	1.058	11474
X-RAY DIFFRACTION	f_dihedral_angle_d	15.58	3177
X-RAY DIFFRACTION	f_chiral_restr	0.069	1384
X-RAY DIFFRACTION	f_plane_restr	0.005	1492

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.8-1.8205	0.3599	152	0.3227	2975	98
1.8205-1.8419	0.3346	168	0.3	3078	100
1.8419-1.8644	0.3456	140	0.2834	3069	100
1.8644-1.888	0.3394	158	0.2611	3083	100
1.888-1.9128	0.2862	158	0.2569	3074	100
1.9128-1.939	0.2967	173	0.2509	3014	100
1.939-1.9667	0.256	164	0.2401	3126	100
1.9667-1.996	0.2831	152	0.2237	3042	100
1.996-2.0272	0.2525	177	0.2191	3064	100
2.0272-2.0605	0.2719	158	0.2136	3040	100
2.0605-2.096	0.2652	136	0.2068	3066	100
2.096-2.1341	0.2787	168	0.2004	3081	100
2.1341-2.1751	0.2396	158	0.2021	3072	100
2.1751-2.2195	0.2295	151	0.1884	3096	100
2.2195-2.2678	0.2331	178	0.1781	3084	100
2.2678-2.3205	0.2349	161	0.1841	3010	100
2.3205-2.3785	0.2567	157	0.1854	3058	100
2.3785-2.4428	0.2205	159	0.186	3027	100
2.4428-2.5147	0.2383	161	0.19	3053	100
2.5147-2.5958	0.2207	152	0.1857	3122	100
2.5958-2.6885	0.2181	160	0.182	3058	100
2.6885-2.7961	0.2408	156	0.1835	3087	100
2.7961-2.9233	0.1983	184	0.1869	3022	100
2.9233-3.0773	0.2458	151	0.193	3081	100
3.0773-3.2699	0.2222	159	0.1913	3053	100
3.2699-3.5221	0.2184	174	0.1856	3056	100
3.5221-3.876	0.2181	176	0.1748	3028	100
3.876-4.4356	0.2071	165	0.1516	3081	100
4.4356-5.5836	0.1926	159	0.1718	3066	100
5.5836-32.1118	0.1798	153	0.1813	3024	99

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	4.1837	-0.0872	-1.4949	5.9544	0.5923	1.9062	0.0136	-0.4729	-0.103	0.6989	0.1113	-0.0698	0.0073	0.688	-0.0198	0.2187	0.0202	0.031	0.3405	-0.0742	0.265	-24.7321	-24.6392	-2.265
2	2.1724	-0.2978	-0.5178	2.7206	-0.0174	0.8871	0.0012	-0.1226	0.1357	0.191	0.0255	-0.3964	0.0575	0.0308	-0.0032	0.1799	-0.0159	-0.0466	0.2245	-0.0062	0.0615	-23.9769	-15.3506	1.2228
3	2.962	0.0732	0.0842	2.0439	0.0346	2.3709	0.0895	-0.5039	-0.0004	0.4311	-0.0689	-0.0553	-0.0407	-0.2129	-0.0172	0.2189	-0.0427	0.0024	0.3092	0.0131	0.0792	-26.0045	-16.3727	5.7225
4	1.712	0.2023	0.8728	0.9336	0.0517	3.85	0.0121	-0.0354	-0.2579	0.0068	-0.1184	0.0608	0.2354	-0.1131	0.0399	0.1889	-0.0293	0.0193	0.2925	-0.0536	0.0922	-34.3539	-19.6899	0.0161
5	1.3135	0.5866	-0.049	4.3459	1.7642	3.6335	-0.0377	0.3202	-0.1964	-0.4545	-0.0965	0.1614	0.1019	-0.2484	0.2132	0.1726	-0.0345	-0.0195	0.2812	-0.0992	0.2398	-40.4088	-25.6814	-13.1238
6	5.527	-0.2341	-1.2876	1.6033	-1.063	3.7862	-0.2049	-0.5402	-1.1396	0.4498	0.0611	0.1974	0.0704	-0.5651	0.0595	0.2674	-0.1119	0.0445	0.428	0.0705	0.1834	-40.2614	-24.2186	5.5001
7	2.8045	-0.9874	2.2826	0.4975	-0.368	3.2118	-0.0593	0.2072	-0.0644	0.1745	0.2224	-0.6401	-0.6033	0.7806	0.088	0.2601	-0.0759	-0.0014	0.3274	-0.0257	0.4331	3.066	-26.5597	-2.5913
8	2.1985	-0.4507	-0.8912	9.0813	7.0558	5.7094	-0.0388	-0.2779	-0.5176	-0.3219	0.1176	-0.5397	-0.2824	0.4185	-0.0558	0.2087	0.0228	-0.033	0.2026	0.0452	0.4366	2.3791	-23.0962	3.8163
9	1.9304	0.7221	-0.5045	1.2802	0.1753	0.634	0.1524	-0.1905	0.3339	0.1185	0.1748	0.0081	-0.1415	-0.1277	-0.3141	0.1752	0.0184	-0.0204	0.2345	0.0075	0.2972	-7.7026	-17.698	3.8453
10	4.132	0.3007	-1.2965	3.6047	0.0654	2.5632	0.1867	-0.7355	0.1908	0.5382	0.0523	0.3846	-0.1849	-0.2026	-0.128	0.238	0.0066	-0.0252	0.3808	0.0449	0.2106	-6.959	-21.6312	13.9277
11	0.1327	0.1722	-0.5101	3.3246	-2.8774	3.4433	-0.0071	-0.1752	-0.0993	0.1431	-0.0887	-0.2586	-0.0009	0.189	0.2355	0.1532	-0.0122	-0.025	0.2455	0.037	0.2148	-2.2586	-24.1744	1.2346
12	1.898	-0.1997	0.5541	2.7659	1.0272	4.6492	0.125	-0.0916	-0.2651	0.1859	-0.1447	-0.0759	0.3908	-0.0124	0.0016	0.1822	-0.0273	0.0053	0.1075	0.045	0.2574	-6.8867	-32.5791	0.5109
13	2.4918	1.5224	0.2021	1.6299	0.0795	0.24	-0.5384	-0.0197	-0.7123	-0.6883	-0.3635	-1.2129	0.5941	0.5775	0.1869	0.3283	0.0994	0.1629	0.2759	0.0873	0.4376	2.9777	-34.9747	-12.203
14	1.2858	-0.3078	0.7568	3.717	-0.5629	5.0656	0.1569	-0.0358	-0.3044	0.044	-0.2801	-0.4355	0.1876	0.1407	0.1104	0.1907	0.0096	0.016	0.1631	0.0231	0.577	-3.5273	-38.565	-4.9089
15	8.9624	-0.3215	4.6918	0.4449	-1.0006	4.8421	1.2932	1.395	-0.3695	-1.022	-0.4984	-0.0817	0.4273	0.6355	-0.7028	0.6397	0.161	0.0939	0.3121	-0.0713	0.7015	-2.3523	-43.1394	-14.2838
16	0.7653	0.3713	1.2505	1.4871	1.1244	4.9035	0.1115	-0.2278	-0.7379	0.2629	0.0397	-0.3084	0.3767	0.0998	-0.174	0.2676	-0.0205	-0.0256	0.1846	0.0862	0.4237	-6.0606	-39.0283	3.4813
17	2.2226	-0.4632	-0.5913	2.7586	0.0285	2.4948	0.1248	-0.0693	0.3619	0.01	-0.0709	0.2056	-0.0928	0.0756	-0.1609	0.1716	-0.0083	0.0286	0.2343	-0.0205	0.2849	11.2372	-4.0064	4.0156
18	2.3895	-0.461	0.4326	2.5004	0.2024	3.3176	0.0376	-0.3764	-0.0395	0.4564	0.0384	0.0454	0.15	0.1281	-0.1015	0.2232	0.0034	0.0327	0.2424	0.0172	0.1849	13.7331	-6.1248	10.2577
19	3.5173	-0.077	-0.4655	2.0712	0.9097	1.7902	-0.0727	0.1491	-0.2594	0.0643	0.1711	-0.334	0.0271	0.2552	-0.083	0.145	0.0223	-0.0442	0.2692	-0.0137	0.2409	24.9775	-14.2321	-0.8267
20	0.2258	0.2453	-0.013	3.6544	2.0629	1.6367	-0.1166	0.4032	0.5202	-0.0674	-0.3286	0.4586	0.1432	-0.7048	0.2961	0.2609	-0.0283	-0.0165	0.3809	-0.0439	0.5272	6.0715	23.8716	-0.2908
21	0.6531	-0.4503	-0.1473	1.7782	1.3127	1.0863	0.0963	0.026	0.2671	-0.0617	-0.0117	-0.1124	-0.7726	0.1554	-0.217	0.1797	-0.0592	0.0276	0.3239	-0.0347	0.4944	2.1894	22.4525	4.8572
22	0.3863	0.1558	-0.6309	0.6982	-1.1138	2.2004	-0.149	-0.1068	-0.6622	0.1185	-0.042	0.2129	0.1025	-0.622	-0.0586	0.2637	0.0021	0.0419	0.3695	0.021	0.3472	-3.9633	12.576	6.3995
23	2.5135	-2.5226	1.2329	3.0293	-1.941	2.2175	-0.106	-0.1022	-0.0485	0.0668	0.0579	0.2396	-0.0084	-0.327	0.0217	0.1732	-0.0129	0.037	0.2363	-0.0347	0.3144	6.7019	9.6141	6.9597
24	4.4816	0.9184	1.8326	2.846	-1.0934	3.9565	0.2666	-0.7311	-0.3256	0.5202	-0.0928	0.1455	0.2776	-0.2533	-0.3163	0.278	0.0425	0.027	0.3332	-0.081	0.422	2.2066	13.1395	17.2082
25	1.8076	0.499	0.6921	1.3371	0.3275	2.5004	-0.0076	-0.1648	0.2674	0.145	0.0209	-0.0035	-0.1705	-0.0751	0.1371	0.208	0.0107	-0.0345	0.2496	-0.0143	0.3395	5.0899	19.0261	4.0882
26	2.1574	1.0243	-1.7588	1.9756	-0.092	2.3381	-0.1189	0.0064	0.4357	-0.0724	0.046	-0.3352	-0.2364	-0.0375	-0.002	0.1705	-0.0265	-0.0887	0.2345	-0.019	0.4199	14.8794	22.7186	1.3033
27	1.4013	2.4167	-1.2393	4.8732	-3.5906	4.8391	-0.1564	0.2524	-0.0518	-0.4621	-0.1906	-0.5138	0.1376	0.4815	0.2458	0.2309	-0.0332	-0.0118	0.3441	0.0184	0.561	23.6442	24.5501	-2.074
28	1.3087	1.1893	1.252	3.9061	2.6587	7.7124	-0.2442	-0.7372	0.7151	0.5518	-0.111	-0.4062	-0.5404	0.3687	-0.0564	0.2622	-0.0545	-0.1495	0.3577	-0.0675	0.5069	16.3628	23.0177	14.6336
29	2.1884	-1.4597	-0.0253	1.3629	-0.113	0.0385	0.0305	0.1534	0.3076	0.0158	0.1273	0.2213	-0.1471	-0.2549	-0.0371	0.1729	-0.0255	-0.0315	0.2389	-0.0383	0.4295	-26.2544	25.4027	1.74
30	2.0277	-0.5841	-0.0258	2.0896	-0.0269	2.3625	0.0963	-0.4608	0.052	0.1558	0.1904	-0.3089	0.1148	0.0729	-0.3357	0.1292	0.0182	-0.0503	0.2374	-0.0476	0.2207	-13.9235	18.4538	6.9581
31	1.4919	0.3917	0.3128	2.8589	0.9851	7.0898	0.1992	-0.5943	0.0965	0.6189	0.5572	-0.0958	0.388	-0.4226	-0.0151	0.306	0.0623	-0.0926	0.2827	-0.1247	0.2723	-20.2838	16.9057	13.9847
32	0.016	-0.0877	0.1258	4.6189	2.7258	5.1517	-0.2691	-0.193	0.1462	-0.3531	0.2913	0.0451	-0.2098	-0.1149	-0.3612	0.1656	0.0282	0.0039	0.1988	-0.0171	0.2842	-19.584	20.4271	-7.3745
33	1.6189	-0.3619	-2.1396	2.0535	-1.1107	3.9601	0.0125	-0.046	0.6191	0.1844	0.0777	-0.256	-0.1226	-0.1352	-0.0182	0.1922	0.0095	-0.0863	0.2217	-0.0821	0.4594	-16.2142	29.5584	4.8368
34	3.3257	0.1914	-1.8119	2.9451	0.0582	7.6884	0.2804	1.1378	1.1069	-0.2682	-0.0511	-0.1437	-0.7836	-0.6952	-0.3063	0.2739	-0.0044	0.0871	0.4289	0.1524	0.7413	-22.4912	36.4087	-9.7167
35	1.6562	-0.2167	0.4656	0.2973	1.2932	7.0666	0.1673	0.5303	0.7201	-0.0913	0.2961	-0.5113	-1.0512	0.3079	-0.2014	0.3482	-0.0572	0.083	0.2997	0.0114	0.9535	-11.3134	40.6067	-5.8511
36	4.6511	-3.2731	2.4224	2.5016	-2.6035	5.3753	0.6571	0.7223	0.4763	-0.1486	0.0838	1.0246	-0.4702	-0.0215	-0.0243	0.2695	-0.0144	-0.0064	0.4048	0.1869	1.1063	-17.5384	43.0208	-4.5009
37	0.2057	0.5047	0.3867	3.7813	3.2234	2.7231	-0.0671	-0.0286	-0.5295	0.2689	-0.0665	0.2918	0.3238	-0.0692	0.0573	0.3046	0.0016	0.0175	0.261	-0.0654	0.4289	-17.3777	38.8467	16.4821
38	1.1054	-0.3196	1.5964	0.4203	-0.3437	3.6313	-0.0864	-0.0206	-0.1501	-0.1931	0.1446	0.1252	0.8341	-0.0474	-0.1439	0.2842	-0.0301	-0.0515	0.2691	-0.0076	0.3025	-37.4819	1.2472	-7.1442
39	1.2786	0.1856	-0.1266	2.3655	-0.3972	2.1027	0.0832	-0.2376	0.2108	0.2136	-0.0286	-0.0951	0.0976	0.0351	-0.0029	0.1697	-0.0087	-0.0392	0.2257	-0.0328	0.1426	-29.873	3.9216	2.5202
40	1.8634	-0.0505	1.2035	0.9444	-1.0063	1.7664	0.0349	-0.5643	0.3777	0.6335	0.2918	-0.3625	0.0927	0.0026	-0.3286	0.3321	0.0305	-0.024	0.3765	-0.0893	0.1947	-32.2359	4.407	12.9485
41	1.6842	0.3099	0.1564	2.237	-0	1.4815	0.0899	-0.3926	0.3734	0.0663	0.0941	0.3324	-0.0007	-0.1334	-0.0012	0.1698	0.0012	-0.0226	0.2631	-0.0267	0.1762	-39.0964	3.8232	-0.5387
42	3.7316	-0.129	2.3404	1.1714	-0.6634	5.7481	-0.1831	-0.08	0.4698	-0.0517	0.0362	0.2111	-0.5339	-0.3457	0.1265	0.2217	0.0217	-0.053	0.2382	-0.0152	0.2599	-35.4065	17.1048	-3.5663
43	6.0794	2.7683	-0.0111	8.5513	-0.1851	4.412	0.0418	0.2457	0.4158	-0.4244	0.0971	0.33	-0.0178	-0.3401	-0.0815	0.1554	0.0198	-0.098	0.2796	0.016	0.3547	-45.7772	10.0873	-11.8684
44	2.6383	-1.111	1.6682	1.6953	-1.0662	8.1166	-0.1245	0.0023	0.2873	-0.0942	-0.0279	0.533	-0.0541	-0.5874	0.0679	0.203	0.0332	-0.0429	0.3098	-0.0098	0.4462	-48.2297	14.5195	-6.8937

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 591:606 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 607:647 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 648:680 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 681:718 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 719:762 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 763:775 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 593:607 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 608:619 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 620:647 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 648:669 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 670:693 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 694:718 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 719:728 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 729:740 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 741:754 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 755:773 )
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESID 594:647 )
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESID 648:703 )
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESID 704:775 )
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESID 594:606 )
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESID 607:619 )
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESID 620:631 )
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 632:648 )
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESID 649:668 )
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESID 669:693 )
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESID 694:732 )
27	X-RAY DIFFRACTION	27	CHAIN D AND (RESID 733:762 )
28	X-RAY DIFFRACTION	28	CHAIN D AND (RESID 763:775 )
29	X-RAY DIFFRACTION	29	CHAIN E AND (RESID 587:619 )
30	X-RAY DIFFRACTION	30	CHAIN E AND (RESID 620:652 )
31	X-RAY DIFFRACTION	31	CHAIN E AND (RESID 653:669 )
32	X-RAY DIFFRACTION	32	CHAIN E AND (RESID 670:680 )
33	X-RAY DIFFRACTION	33	CHAIN E AND (RESID 681:718 )
34	X-RAY DIFFRACTION	34	CHAIN E AND (RESID 719:732 )
35	X-RAY DIFFRACTION	35	CHAIN E AND (RESID 733:746 )
36	X-RAY DIFFRACTION	36	CHAIN E AND (RESID 747:762 )
37	X-RAY DIFFRACTION	37	CHAIN E AND (RESID 763:784 )
38	X-RAY DIFFRACTION	38	CHAIN F AND (RESID 594:609 )
39	X-RAY DIFFRACTION	39	CHAIN F AND (RESID 610:648 )
40	X-RAY DIFFRACTION	40	CHAIN F AND (RESID 649:668 )
41	X-RAY DIFFRACTION	41	CHAIN F AND (RESID 669:703 )
42	X-RAY DIFFRACTION	42	CHAIN F AND (RESID 704:718 )
43	X-RAY DIFFRACTION	43	CHAIN F AND (RESID 719:740 )
44	X-RAY DIFFRACTION	44	CHAIN F AND (RESID 741:773 )

-
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