PDB-6qyy: The crystal structure of head fiber gp8.5 N base in bacteriophage...

ID or keywords:

Entry

Database: PDB / ID: 6qyy

Title

The crystal structure of head fiber gp8.5 N base in bacteriophage phi29

Components

Capsid fiber protein

Keywords

VIRUS /

bacteriophage / phi29 /

prohead

Function / homology

viral capsid, fiber / Bacteriophage B103, Gp8, head fibre / Head fiber protein / viral procapsid / symbiont entry into host cell / virion attachment to host cell / identical protein binding / Capsid fiber protein

Function and homology information

Biological species

Bacillus phage phi29 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Xu, J. / Wang, D. / Gui, M. / Xiang, Y.

Funding support

China, 3items

Organization	Grant number	Country
Ministry of Science and Technology (China)	2016YFA0501100	China
Ministry of Science and Technology (China)	2015CB910102	China
National Natural Science Foundation of China	31470721	China

Citation

Journal: Nat Commun / Year: 2019
Title: Structural assembly of the tailed bacteriophage ϕ29.
Authors: Jingwei Xu / Dianhong Wang / Miao Gui / Ye Xiang /

Abstract: The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile ...

History

Deposition	Mar 10, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release
Revision 2.0	Oct 2, 2019	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary Category: atom_site / cell ...atom_site / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _atom_site.label_entity_id / _cell.Z_PDB ..._atom_site.label_entity_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.ref_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6qyy.cif.gz	295 KB	Display	PDBx/mmCIF format
PDB format	pdb6qyy.ent.gz	252.9 KB	Display	PDB format
PDBx/mmJSON format	6qyy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qy/6qyy ftp://data.pdbj.org/pub/pdb/validation_reports/qy/6qyy	HTTPS FTP

-
Related structure data

Related structure data	4655C 4662C 4677C 4678C 4679C 4680C 4681C 4682C 4683C 4684C 4685C 6qvkC 6qx7C 6qydC 6qyjC 6qymC 6qyzC 6qz0C 6qz9C 6qzfC C: citing same article (ref.)
Similar structure data	5aao-5 5aao-6 4x9d-d 3rer-d 5aao-4 5yz2-d 5s8o-d 4g3u-1 4x9c-d 4ht8-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Capsid fiber protein

B: Capsid fiber protein

C: Capsid fiber protein

D: Capsid fiber protein

E: Capsid fiber protein

F: Capsid fiber protein

hetero molecules

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

1

A: Capsid fiber protein

C: Capsid fiber protein

E: Capsid fiber protein

hetero molecules

defined by author&software
Evidence: assay for oligomerization
39 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Capsid fiber protein

F: Capsid fiber protein

hetero molecules

B: Capsid fiber protein

hetero molecules

defined by author&software
39 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.212, 65.070, 118.874
Angle α, β, γ (deg.)	90.00, 99.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Capsid fiber protein / Gene product 8.5 / gp8.5 / Head fiber protein / Protein p8.5 Mass: 12861.392 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus) / Gene: 8.5 / Production host: Escherichia coli (E. coli) / References: UniProt: B3VMP4
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄ / References: UniProt: B3VMP4*PLUS
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.76 Å³/Da / Density % sol: 55.39 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 6.0), 0.15 Ammonium sulfate, 4% (v/v) DMSO

-
Data collection

Diffraction	Mean temperature: 63 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 1, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 1.8→41.79 Å / Num. obs: 76833 / % possible obs: 99.31 % / Redundancy: 3.4 % / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.8→1.864 Å

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→41.79 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.79

	R_factor	Num. reflection	% reflection
R_free	0.2239	3858	5.03 %
R_work	0.1825	-	-
obs	0.1846	76776	99.32 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→41.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5356	0	40	583	5979

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5510
X-RAY DIFFRACTION	f_angle_d	0.866	7508
X-RAY DIFFRACTION	f_dihedral_angle_d	3.838	4306
X-RAY DIFFRACTION	f_chiral_restr	0.061	896
X-RAY DIFFRACTION	f_plane_restr	0.004	968

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 (%)
1.8-1.822	0.3271	123	0.3293	2579	X-RAY DIFFRACTION	99
1.822-1.845	0.3888	152	0.3136	2616	X-RAY DIFFRACTION	100
1.845-1.8693	0.3288	115	0.3042	2572	X-RAY DIFFRACTION	99
1.8693-1.8949	0.3179	154	0.2844	2617	X-RAY DIFFRACTION	100
1.8949-1.922	0.3468	131	0.2669	2576	X-RAY DIFFRACTION	99
1.922-1.9507	0.3029	122	0.2516	2603	X-RAY DIFFRACTION	100
1.9507-1.9811	0.2963	131	0.2444	2652	X-RAY DIFFRACTION	99
1.9811-2.0136	0.2773	143	0.2455	2539	X-RAY DIFFRACTION	100
2.0136-2.0483	0.2908	150	0.2401	2647	X-RAY DIFFRACTION	99
2.0483-2.0856	0.244	136	0.2163	2591	X-RAY DIFFRACTION	100
2.0856-2.1257	0.2371	132	0.2108	2589	X-RAY DIFFRACTION	100
2.1257-2.1691	0.2581	117	0.2083	2625	X-RAY DIFFRACTION	100
2.1691-2.2163	0.2551	126	0.2016	2597	X-RAY DIFFRACTION	99
2.2163-2.2678	0.2724	136	0.2083	2588	X-RAY DIFFRACTION	100
2.2678-2.3245	0.2903	153	0.2086	2620	X-RAY DIFFRACTION	99
2.3245-2.3874	0.228	125	0.2188	2605	X-RAY DIFFRACTION	100
2.3874-2.4576	0.2973	160	0.2145	2557	X-RAY DIFFRACTION	99
2.4576-2.5369	0.2622	155	0.2114	2575	X-RAY DIFFRACTION	99
2.5369-2.6276	0.2647	143	0.2035	2626	X-RAY DIFFRACTION	99
2.6276-2.7328	0.2569	139	0.1951	2586	X-RAY DIFFRACTION	100
2.7328-2.8572	0.2323	139	0.1936	2607	X-RAY DIFFRACTION	99
2.8572-3.0078	0.2394	135	0.1992	2605	X-RAY DIFFRACTION	99
3.0078-3.1962	0.2494	136	0.1917	2593	X-RAY DIFFRACTION	99
3.1962-3.4429	0.2104	143	0.1665	2639	X-RAY DIFFRACTION	99
3.4429-3.7892	0.2057	153	0.1565	2590	X-RAY DIFFRACTION	100
3.7892-4.3372	0.1638	146	0.1302	2646	X-RAY DIFFRACTION	100
4.3372-5.4631	0.135	136	0.1239	2648	X-RAY DIFFRACTION	99
5.4631-46.7221	0.1845	127	0.156	2630	X-RAY DIFFRACTION	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	5.3085	2.0165	5.1102	8.6332	1.5947	4.8923	-0.1163	0.2716	0.2601	-0.4092	-0.0728	0.0453	1.2792	-0.0413	0.3492	0.2779	0.0193	0.0164	0.2808	0.0082	0.2637	-16.372	15.8218	123.3492
2	5.9817	-0.1936	2.1735	4.613	-6.156	9.3092	0.035	-0.2204	0.188	0.6602	0.1239	-0.0003	-0.4374	0.35	-0.1328	0.294	-0.0019	-0.0149	0.2334	-0.0471	0.2263	-12.4017	28.4899	130.4286
3	9.0452	3.6454	-1.783	3.7307	2.692	5.4256	-0.067	-0.198	-0.7872	0.8059	-0.2704	-0.6783	0.7024	0.5397	0.2872	0.3596	0.0868	-0.0311	0.3491	0.0197	0.2464	-7.9326	16.9574	130.19
4	5.6905	5.215	0.1262	9.2101	1.243	5.4695	0.0685	-0.309	-0.2236	0.3414	0.1801	-1.089	0.3271	0.7007	-0.1084	0.1554	0.0075	-0.0299	0.3017	-0.017	0.3558	-3.7785	27.2947	123.6975
5	7.8273	-2.6143	-0.0226	9.2601	-5.0368	3.0481	-0.2953	-0.4649	0.2381	0.8915	0.3822	0.3134	-0.51	-1.1558	-0.0645	0.3291	-0.0102	0.0119	0.2444	-0.0424	0.267	-16.9761	24.013	132.7882
6	0.1381	0.554	-0.7408	2.6361	1.2175	9.3092	-0.3017	-0.064	-0.0589	-0.3928	0.2563	0.0998	0.4948	0.0602	-0.0007	0.1289	0.0327	-0.0014	0.1993	-0.0049	0.2577	-15.2035	24.4512	119.9088
7	4.0973	-0.4018	0.0736	4.9162	-0.2436	6.1484	0.1116	-0.2177	0.2197	0.2659	-0.2361	-0.893	-0.6348	0.7131	0.0103	0.2189	-0.1235	-0.0149	0.3107	-0.055	0.3851	-2.4132	37.9258	121.1402
8	8.8262	-2.3288	-4.6181	8.9331	3.463	8.1456	0.0798	0.0122	0.506	-0.072	-0.0978	0.3943	-0.798	-0.1841	0.026	0.2753	-0.0788	0.0021	0.2373	-0.0636	0.3411	-8.9612	39.9433	118.0259
9	6.5361	-3.0102	-5.1739	2.6941	4.9416	9.3856	-0.0675	0.4007	-0.2353	-0.1669	-0.2581	0.5226	0.3842	-0.6133	-0.006	0.253	-0.0139	0.0103	0.2283	-0.0487	0.3093	-11.0541	34.8067	115.8271
10	3.53	1.7067	-0.6823	2.4208	2.2388	4.2744	-0.3267	0.4871	-1.1406	-1.491	-0.3072	-2.4972	0.0362	1.0383	0.4698	0.4351	0.0845	0.1061	0.6469	-0.0027	0.7389	0.6367	32.8684	111.0728
11	6.9816	2.1416	4.727	8.9572	3.4308	3.6727	0.0081	0.2613	0.2859	0.0858	-0.4097	0.3414	1.6506	-0.0724	0.2675	0.3589	0.0638	0.0953	0.2617	0.0462	0.3229	-7.0968	-15.1017	64.4954
12	7.4395	-1.8895	2.698	3.6465	-5.0867	7.3478	-0.2857	-0.4981	0.3195	0.7803	0.4424	0.0946	0.1323	-0.5369	-0.0708	0.3933	0.0207	0.0062	0.3429	-0.0886	0.2644	-3.1123	-2.4701	72.3351
13	7.923	2.7945	-0.3687	8.6992	0.0487	5.8393	-0.1613	-0.4058	-0.2974	0.6243	-0.0474	-0.5212	0.6643	0.7529	0.2458	0.3141	0.0799	-0.0199	0.3616	0.009	0.2319	2.9809	-9.7617	68.7967
14	9.2706	-2.1323	3.4442	2.8611	0.7176	4.187	-0.5648	-1.2361	0.7269	1.2466	0.0411	0.6209	-0.4704	-0.6263	0.0627	0.4856	0.0374	0.0915	0.4936	-0.0623	0.4345	-7.7233	-6.83	74.0448
15	4.5307	2.5496	-2.5454	7.3652	-5.6524	4.4397	0.1602	-0.1458	0.533	0.5822	-0.0122	0.5987	-0.0173	0.0137	-0.2436	0.3689	0.0288	0.09	0.2943	-0.009	0.3674	-8.4831	-12.6843	66.1482
16	4.9752	1.7631	2.5128	9.1854	4.9828	7.969	-0.1958	-0.2953	-0.104	-0.7649	-0.0129	0.2134	0.1191	-0.2417	0.259	0.3309	-0.033	-0.0003	0.291	-0.0062	0.2472	-4.1579	-2.1327	57.8888
17	4.4449	-0.9006	-0.3394	6.735	-1.5844	7.1538	0.0104	-0.0788	0.2928	0.15	-0.0585	-1.0641	-0.7034	1.0219	0.0387	0.3102	-0.148	-0.025	0.4351	-0.0784	0.473	7.0581	7.0056	62.5213
18	8.9684	-3.9078	-4.5272	7.0941	4.793	3.8021	-0.2059	-0.1431	0.3807	-0.087	0.1094	0.2449	-0.6938	-0.0533	0.0132	0.4239	-0.0143	-0.0016	0.3418	-0.0515	0.3661	0.5639	9.064	59.4232
19	5.6321	1.6682	-1.9342	7.0481	-0.6682	2.4471	-0.3542	0.3467	0.1074	-0.8711	0.3404	-1.1669	-0.1666	0.6962	0.076	0.3535	-0.0501	0.0584	0.4529	-0.067	0.4019	3.9436	2.9503	54.9619
20	6.4557	3.6904	-4.3279	3.1049	-2.6944	3.4561	0.2098	-0.3035	0.5215	0.8935	0.1978	0.9885	-0.5536	-0.0206	-0.372	0.3536	0.0029	0.0496	0.2343	-0.0376	0.3503	-14.1841	39.168	106.1121
21	5.9969	-0.6678	-3.6209	3.3429	-0.3115	6.6558	-0.1007	0.5584	0.3228	-1.3355	-0.0287	-0.378	-0.1038	0.2415	0.156	0.4343	-0.0565	-0.0212	0.2321	0.0358	0.2043	-7.3232	38.2082	92.1059
22	6.2237	-0.1739	-0.0162	5.606	0.7226	4.2001	0.0362	-0.2308	0.5144	0.1576	0.0147	-0.6671	-0.4643	0.5113	-0.0856	0.2907	-0.0961	-0.001	0.2758	-0.0165	0.2925	-3.3043	38.5325	101.2892
23	7.7553	5.3212	6.6389	5.1476	6.467	8.3943	-0.5665	0.0903	0.9235	-1.5016	-0.0353	0.821	-0.8594	-0.1953	0.4806	0.4084	-0.0653	-0.0443	0.2549	0.0203	0.3069	-11.9931	42.932	93.5672
24	2.274	-0.7711	-0.576	8.6246	-3.0999	4.2619	-0.083	0.0928	0.2181	0.1207	0.1049	0.6536	-0.0457	-0.1237	-0.0024	0.1273	-0.0336	-0.0399	0.1745	-0.0109	0.1886	-13.1638	32.1016	100.1495
25	5.0046	1.3271	-0.1627	8.3934	1.3321	4.8502	0.0946	0.346	-0.0386	-0.5304	0.1042	-1.0148	-0.3772	0.6251	-0.1702	0.2916	-0.0643	0.1237	0.3794	-0.0201	0.3605	2.2039	24.587	90.7865
26	6.572	-0.6932	2.6596	6.3191	-1.7242	6.4204	-0.2272	0.5893	0.1011	-0.8499	0.2289	-0.3478	-0.4137	0.0849	0.0753	0.3289	-0.0491	0.058	0.2194	-0.0181	0.1898	-4.4512	21.5229	89.5329
27	7.6982	-0.8749	-0.7537	7.4896	0.1543	9.3164	0.0186	-0.3143	0.051	0.3463	0.0573	-1.1463	-0.202	0.6801	-0.0176	0.2048	-0.0364	-0.0294	0.1768	0.0076	0.3172	-2.677	20.61	97.5775
28	9.6078	4.9276	-3.0272	5.2257	-4.218	3.5416	0.0583	0.1895	0.5815	0.5874	-0.1309	-0.3796	-0.1677	0.828	-0.0747	0.4176	-0.0522	0.0308	0.4315	-0.0455	0.264	-14.1223	17.9937	80.229
29	8.8729	-1.1236	1.5763	2.6824	-2.1454	2.2578	-0.0303	0.1337	-0.5623	0.5653	-0.2363	-0.3267	1.134	0.5516	0.221	0.6184	0.0374	-0.0124	0.2949	-0.0417	0.3331	-15.9729	3.4409	73.1045
30	5.1616	-1.9013	1.67	7.2969	1.1188	0.9762	-0.1023	-0.6934	-0.3039	0.5187	0.2133	0.4955	1.4221	-0.9121	-0.0616	0.3931	-0.0512	0.0377	0.3988	0.0149	0.2139	-21.9132	8.9131	81.0991
31	8.6525	3.1247	3.1335	9.0825	1.1748	6.411	-0.211	-0.0534	-0.2668	-0.0451	0.1016	0.5676	0.6339	-0.7311	0.1058	0.2995	-0.1154	0.0183	0.3782	-0.0006	0.2217	-24.7833	8.2609	68.8715
32	3.0795	-1.1948	2.1484	7.527	1.5949	8.9562	-0.0504	0.1359	-0.2733	0.385	0.2983	-0.6825	1.0016	1.1189	-0.1985	0.4779	0.1043	0.0107	0.5272	-0.0719	0.3544	-11.6532	7.1129	78.6127
33	0.8222	-0.6133	0.3837	3.5667	1.1414	4.8704	0.0184	-0.2188	0.0287	-0.0379	0.09	0.0692	-0.4208	0.6488	-0.1275	0.3069	-0.0881	0.0032	0.3586	-0.0138	0.2762	-15.7786	15.8107	66.2215
34	8.9047	-0.7264	2.6211	5.1674	-5.7842	7.0654	-0.1066	0.6099	-0.3871	-0.8657	0.1597	0.321	0.8789	-0.4243	-0.0019	0.4441	-0.0637	-0.0668	0.3581	-0.0353	0.3053	-22.0052	4.7341	53.3569
35	3.1964	-4.6785	-0.3437	7.5423	0.6535	5.8735	-0.1343	-0.0325	-0.2815	0.4997	0.0713	0.5271	0.5904	-1.0324	-0.0837	0.389	-0.1759	-0.0094	0.4967	-0.0113	0.3355	-27.262	4.3554	61.5156
36	7.4277	1.096	-5.8228	5.2794	-1.7829	4.7397	0.0574	0.2792	-0.033	0.201	-0.2374	0.2508	-0.5879	-0.6245	0.1914	0.2882	-0.0334	-0.0493	0.3384	-0.0282	0.2631	-25.0908	12.5231	58.2337
37	7.8447	-5.7155	4.7642	4.9078	-4.1346	3.4967	0.2347	0.5068	-0.7692	-1.0136	0.0819	0.1254	0.8434	0.4639	-0.3061	0.397	0.0167	-0.013	0.3717	-0.052	0.4093	-15.4965	3.8293	53.781
38	2.1187	1.7388	-1.1419	2.1889	0.1383	9.8356	-0.0145	-0.0393	0.3873	0.0032	0.1855	-0.3823	0.2495	0.0099	-0.1371	0.2161	-0.0484	-0.0296	0.2591	-0.0193	0.2357	-17.9074	12.0963	58.5925
39	5.5459	0.3211	-5.9733	0.0152	-0.3392	6.4451	1.8895	0.9343	-0.2986	2.4005	0.2946	-0.5325	-0.9426	-0.8817	-1.8863	0.8597	-0.0844	-0.0448	0.5165	0.0212	0.8485	-25.5379	21.85	63.4879
40	2.863	0.4088	1.0128	6.8553	-1.8212	7.4195	0.0561	-0.0201	0.001	-0.4238	0.1893	0.3721	0.4839	-0.2738	-0.1682	0.1216	-0.0241	0.0114	0.1696	-0.0228	0.1842	-13.1856	8.3988	99.9945
41	5.5854	1.0184	0.5932	7.5302	-4.8625	3.4841	-0.1822	0.5907	-0.1274	-0.6262	-0.1123	-0.206	0.7991	0.7612	0.3248	0.2923	0.0378	0.014	0.3068	-0.0322	0.2012	-6.4395	7.8978	94.8264
42	9.3239	-5.3533	2.7605	8.1413	-0.3433	8.51	0.0152	0.3951	-0.1016	0.0582	-0.0996	-0.3823	0.407	0.918	0.0498	0.2393	0.0356	0.0004	0.2893	0.0207	0.2251	-3.3178	6.6193	107.1383
43	5.0117	2.7868	1.5573	2.1883	0.0776	8.8062	-0.067	-0.0064	-0.2343	-0.2578	0.0371	0.3069	0.5817	-0.6297	-0.0355	0.2977	-0.0126	0.0064	0.2662	-0.0018	0.2109	-16.4271	5.1779	97.3753
44	0.328	1.3687	-0.5008	5.6379	-1.2044	3.712	-0.0865	0.1786	0.0168	-0.0709	0.0921	-0.0286	-0.2117	-0.3059	-0.0445	0.189	0.0382	-0.016	0.265	-0.0187	0.2496	-12.4735	14.0701	109.8858
45	4.6447	0.6129	1.9779	7.8869	3.7481	2.4974	-0.0037	-0.417	-0.2366	1.1509	0.0752	-0.403	0.6651	0.1728	-0.0131	0.3076	0.0449	-0.0392	0.2859	0.0316	0.2577	-6.0611	2.9812	123.2007
46	2.0629	1.858	2.1692	8.6818	-2.1213	6.4988	0.0379	0.1668	-0.7186	-0.3836	0.1504	-0.8193	0.4856	1.0349	-0.2215	0.2098	0.1294	0.0088	0.3731	-0.0423	0.3077	-0.7341	2.7208	114.4861
47	7.4799	5.3912	1.5928	8.4283	5.0003	7.8787	0.3898	-0.4473	-0.1557	0.6675	-0.5181	0.0639	0.4398	-0.0301	0.1352	0.1537	0.0832	-0.0568	0.1747	0.0485	0.2361	-8.9001	5.426	120.5019
48	2.0539	1.8192	0.6479	2.175	1.8971	3.755	-0.097	0.1914	0.2524	-0.0475	0.2903	0.2365	0.1009	0.1489	-0.1882	0.154	0.0194	-0.0254	0.196	0.0035	0.2523	-10.2136	10.3562	117.4456
49	9.5647	-7.1838	-7.4698	9.2293	4.6392	6.5912	-0.1504	-0.7184	-0.2504	-0.5564	0.6025	0.6159	0.4873	0.9776	-0.3111	0.6252	0.0596	0.0154	0.5412	0.0072	0.5808	-2.7448	20.1963	112.4048
50	3.3686	-3.5474	-3.0301	8.8779	4.4657	3.1449	0.32	0.7455	0.152	-1.1853	-0.165	-0.5794	-1.1004	-0.454	-0.3672	0.5575	0	0.0375	0.3184	0.0058	0.3663	-13.8997	40.6462	69.8418
51	5.7527	-2.539	-4.6172	3.1144	2.3314	4.0947	0.0205	-0.0328	0.421	0.7015	-0.2238	0.1552	-0.2157	-0.1175	0.1112	0.4073	0.023	-0.0134	0.3074	-0.0505	0.2439	-21.4139	39.8118	83.8569
52	2.3317	2.9509	-1.6597	9.6607	-2.2332	9.7392	0.1219	0.267	0.9304	-0.7679	-0.0399	0.3654	-0.5779	-0.4212	-0.2767	0.4034	0.1143	-0.0145	0.3849	0.0327	0.4532	-23.1511	44.3993	72.4064
53	2.3914	-2.369	-0.5862	8.4349	3.0519	9.5278	0.3817	0.125	-0.1485	-0.3897	-0.5185	0.9941	-0.4306	-1.0219	0.1099	0.3485	0.0554	-0.0274	0.3715	-0.0253	0.3295	-27.8446	33.9719	77.6843
54	7.645	-6.2801	6.0766	6.3851	-6.5661	7.5187	-0.5961	-0.4792	1.2354	1.1961	0.0998	-0.6747	-1.3552	-0.2129	0.4022	0.5126	0.0801	-0.0007	0.29	-0.0132	0.3966	-16.7175	44.7659	82.5066
55	4.0065	-4.2809	-3.5766	5.1888	4.2357	3.4455	-0.0502	-0.3583	0.5547	-1.2317	-0.1083	-0.4176	-0.764	0.2579	-0.1784	0.4965	0.0359	-0.0011	0.2846	0.0353	0.3494	-13.1289	40.951	73.6627
56	6.0064	0.878	-1.9526	6.7811	-2.0237	5.3724	-0.5839	-0.2377	-0.4698	0.1431	0.0339	0.6736	0.7114	-0.2379	0.5278	0.3527	0.0088	0.0909	0.2648	-0.026	0.2925	-22.6312	24.7905	82.6708
57	6.045	-0.3404	2.486	8.596	0.56	5.8921	-0.0329	-0.2982	-0.257	0.0243	-0.434	1.7915	0.1342	-0.9277	0.4951	0.3392	0.0071	0.1422	0.4663	-0.0987	0.5678	-32.7271	28.7115	82.8548
58	6.1337	-1.2397	1.4034	6.7641	4.5028	8.1446	-0.4166	-0.3846	-0.3563	1.1211	0.2406	0.6151	0.9523	0.2294	0.0915	0.5706	-0.0054	0.2034	0.3122	-0.0089	0.3914	-24.5169	22.9235	86.2594
59	2.7184	1.4048	2.3736	6.2316	4.8838	4.4918	-0.2472	-0.2965	-0.1142	-0.0045	0.078	0.2907	0.0221	-0.3631	0.2448	0.4461	0.0157	0.0946	0.2909	-0.0319	0.2594	-21.3505	23.8123	81.5042
60	4.7273	-4.5222	0.2157	5.0786	1.4829	4.1538	0.0031	-0.5353	-0.0353	-1.0487	0.5491	1.427	-0.1783	-1.2744	-0.2777	0.6692	-0.0995	-0.182	0.6225	-0.0214	0.9587	-30.9362	20.1606	74.6932

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 18 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 19 through 32 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 33 through 42 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 43 through 51 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 52 through 66 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 67 through 93 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 94 through 106 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 107 through 112 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 113 through 117 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 9 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 10 through 18 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 19 through 42 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 43 through 51 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 52 through 57 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 58 through 66 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 67 through 93 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 94 through 106 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 107 through 117 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 1 through 9 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 10 through 18 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 19 through 42 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 43 through 51 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 52 through 66 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 67 through 93 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 94 through 106 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 107 through 117 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 1 through 8 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 9 through 18 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 19 through 32 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 33 through 42 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 43 through 55 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 56 through 66 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 67 through 76 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 77 through 93 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 94 through 98 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 99 through 106 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 107 through 112 )
39	X-RAY DIFFRACTION	39	chain 'D' and (resid 113 through 117 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 1 through 18 )
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 19 through 32 )
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 33 through 42 )
43	X-RAY DIFFRACTION	43	chain 'E' and (resid 43 through 55 )
44	X-RAY DIFFRACTION	44	chain 'E' and (resid 56 through 66 )
45	X-RAY DIFFRACTION	45	chain 'E' and (resid 67 through 76 )
46	X-RAY DIFFRACTION	46	chain 'E' and (resid 77 through 93 )
47	X-RAY DIFFRACTION	47	chain 'E' and (resid 94 through 106 )
48	X-RAY DIFFRACTION	48	chain 'E' and (resid 107 through 112 )
49	X-RAY DIFFRACTION	49	chain 'E' and (resid 113 through 117 )
50	X-RAY DIFFRACTION	50	chain 'F' and (resid 1 through 9 )
51	X-RAY DIFFRACTION	51	chain 'F' and (resid 10 through 18 )
52	X-RAY DIFFRACTION	52	chain 'F' and (resid 19 through 32 )
53	X-RAY DIFFRACTION	53	chain 'F' and (resid 33 through 42 )
54	X-RAY DIFFRACTION	54	chain 'F' and (resid 43 through 51 )
55	X-RAY DIFFRACTION	55	chain 'F' and (resid 52 through 57 )
56	X-RAY DIFFRACTION	56	chain 'F' and (resid 58 through 76 )
57	X-RAY DIFFRACTION	57	chain 'F' and (resid 77 through 93 )
58	X-RAY DIFFRACTION	58	chain 'F' and (resid 94 through 106 )
59	X-RAY DIFFRACTION	59	chain 'F' and (resid 107 through 112 )
60	X-RAY DIFFRACTION	60	chain 'F' and (resid 113 through 117 )

-
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