PDB-4ohs: The structure of a far-red fluorescent protein, AQ143

ID or keywords:

Entry

Database: PDB / ID: 4ohs

Title

The structure of a far-red fluorescent protein, AQ143

Components

FAR-RED FLUORESCENT PROTEIN AQ143

Keywords

FLUORESCENT PROTEIN / far-red /

Beta Barrel /

Red Fluorescent Protein / RFP

Function / homology

Green Fluorescent Protein /

Green fluorescent protein / Green fluorescent protein-related /

Green fluorescent protein /

bioluminescence /

Beta Barrel / Mainly Beta / Blue chromoprotein aeCP597

Function and homology information

Biological species

Actinia Equina (sea anemone)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Wannier, T.M. / Mayo, S.L.

Citation

Journal: Protein Sci. / Year: 2014
Title: The structure of a far-red fluorescent protein, AQ143, shows evidence in support of reported red-shifting chromophore interactions.
Authors: Wannier, T.M. / Mayo, S.L.

History

Deposition	Jan 17, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 2, 2014	Group: Database references
Revision 1.2	Aug 6, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ohs.cif.gz	720.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ohs.ent.gz	627.8 KB	Display	PDB format
PDBx/mmJSON format	4ohs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oh/4ohs ftp://data.pdbj.org/pub/pdb/validation_reports/oh/4ohs	HTTPS FTP

-
Related structure data

Similar structure data	6ciu-d 6wem-d 3u8a-d 4edo-3 3svn-d 3svr-d 2gw4-1 1xqm-1 4ljb-d 3pj5-2 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
Related items in Molecule of the Month	#174 - Jun 2014 GFP-like Proteins similarity (3) #42 - Jun 2003 Green Fluorescent Protein similarity (3)

Deposited unit

A: FAR-RED FLUORESCENT PROTEIN AQ143

B: FAR-RED FLUORESCENT PROTEIN AQ143

C: FAR-RED FLUORESCENT PROTEIN AQ143

D: FAR-RED FLUORESCENT PROTEIN AQ143

E: FAR-RED FLUORESCENT PROTEIN AQ143

F: FAR-RED FLUORESCENT PROTEIN AQ143

G: FAR-RED FLUORESCENT PROTEIN AQ143

H: FAR-RED FLUORESCENT PROTEIN AQ143

hetero molecules

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

1

A: FAR-RED FLUORESCENT PROTEIN AQ143

B: FAR-RED FLUORESCENT PROTEIN AQ143

D: FAR-RED FLUORESCENT PROTEIN AQ143

E: FAR-RED FLUORESCENT PROTEIN AQ143

hetero molecules

defined by author&software
107 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: FAR-RED FLUORESCENT PROTEIN AQ143

F: FAR-RED FLUORESCENT PROTEIN AQ143

G: FAR-RED FLUORESCENT PROTEIN AQ143

H: FAR-RED FLUORESCENT PROTEIN AQ143

hetero molecules

defined by author&software
107 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	50.967, 68.114, 132.788
Angle α, β, γ (deg.)	98.38, 90.74, 110.47
Int Tables number	1
Space group name H-M	P1

#1: Protein	FAR-RED FLUORESCENT PROTEIN AQ143 Mass: 26690.262 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Actinia Equina (sea anemone) / References: UniProt: Q2VFP3*PLUS
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2 Å³/Da / Density % sol: 38.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Tris, 50mM lithium sulfate, 20% w/v PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.19→131.1 Å / Num. obs: 72946

-
Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.19→37.326 Å / SU ML: 0.26 / σ(F): 1.97 / Phase error: 30.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2205	3647	5 %
R_work	0.1897	-	-
obs	0.1912	72881	86.08 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.19→37.326 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14128	0	4	355	14487

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	14596
X-RAY DIFFRACTION	f_angle_d	0.987	19737
X-RAY DIFFRACTION	f_dihedral_angle_d	15.675	5398
X-RAY DIFFRACTION	f_chiral_restr	0.041	2031
X-RAY DIFFRACTION	f_plane_restr	0.006	2591

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 (%)
2.19-2.2213	0.3391	60	0.3154	1023	X-RAY DIFFRACTION	33
2.2213-2.2517	0.3429	104	0.2953	2013	X-RAY DIFFRACTION	65
2.2517-2.2839	0.3548	129	0.2898	2334	X-RAY DIFFRACTION	76
2.2839-2.318	0.3374	132	0.2718	2814	X-RAY DIFFRACTION	90
2.318-2.3542	0.3136	161	0.269	2771	X-RAY DIFFRACTION	91
2.3542-2.3928	0.319	165	0.2657	2828	X-RAY DIFFRACTION	91
2.3928-2.4341	0.2976	144	0.2569	2788	X-RAY DIFFRACTION	90
2.4341-2.4783	0.2906	125	0.249	2814	X-RAY DIFFRACTION	91
2.4783-2.526	0.296	147	0.2511	2793	X-RAY DIFFRACTION	90
2.526-2.5775	0.3007	140	0.2478	2755	X-RAY DIFFRACTION	88
2.5775-2.6335	0.2803	122	0.2442	2662	X-RAY DIFFRACTION	87
2.6335-2.6948	0.2824	124	0.238	2686	X-RAY DIFFRACTION	85
2.6948-2.7622	0.291	146	0.2198	2836	X-RAY DIFFRACTION	92
2.7622-2.8368	0.252	159	0.2224	2831	X-RAY DIFFRACTION	91
2.8368-2.9203	0.2665	147	0.236	2795	X-RAY DIFFRACTION	92
2.9203-3.0145	0.257	161	0.2335	2825	X-RAY DIFFRACTION	91
3.0145-3.1222	0.2569	143	0.2252	2706	X-RAY DIFFRACTION	88
3.1222-3.2471	0.2456	120	0.2123	2624	X-RAY DIFFRACTION	84
3.2471-3.3948	0.2538	149	0.1998	2836	X-RAY DIFFRACTION	91
3.3948-3.5736	0.2288	163	0.1795	2814	X-RAY DIFFRACTION	92
3.5736-3.7973	0.2028	165	0.1701	2805	X-RAY DIFFRACTION	91
3.7973-4.0902	0.1888	161	0.1666	2757	X-RAY DIFFRACTION	90
4.0902-4.5012	0.1605	146	0.1393	2674	X-RAY DIFFRACTION	87
4.5012-5.1511	0.1588	159	0.1285	2893	X-RAY DIFFRACTION	93
5.1511-6.4843	0.1676	140	0.1498	2683	X-RAY DIFFRACTION	87
6.4843-37.3317	0.1637	135	0.1661	2874	X-RAY DIFFRACTION	92

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	6.0047	5.3407	-2.2612	7.4179	-3.2441	5.2103	-0.4082	0.1557	0.0012	-0.6717	0.3227	0.6321	0.7451	-0.3983	0.0383	0.4852	-0.0786	0.0054	0.3587	-0.0422	0.3354	29.0613	23.79	25.7943
2	0.5325	-0.0468	-0.5068	2.2945	0.0062	2.5264	-0.0295	-0.0048	0.0153	0.0243	0.0844	0.3412	0.4403	-0.2279	-0.0552	0.4215	-0.0982	0.0752	0.3369	-0.0209	0.3203	30.7371	25.6271	34.6249
3	9.6713	-0.1616	5.4361	4.7813	0.2663	5.0174	0.0536	-0.2464	0.1061	0.3126	-0.1123	0.1735	0.223	0.1134	0.0877	0.4093	-0.0228	0.1358	0.2437	-0.0173	0.2448	35.0216	28.8327	43.0604
4	2.1541	-1.1323	0.5551	4.3077	-0.3556	5.1348	-0.0909	-0.0978	-0.4145	0.2101	0.0731	0.7567	0.4398	-0.2837	-0.0233	0.6956	-0.2151	0.0606	0.3169	-0.0798	0.4986	25.9682	19.9425	40.5158
5	8.6082	4.377	-8.2134	8.0883	-6.5222	2.0893	-0.5073	-0.4745	-0.5407	0.1297	-0.1243	-0.4337	1.0457	0.5368	0.7622	0.4809	-0.0354	-0.0201	0.3881	-0.0147	0.3823	35.4847	17.5214	35.589
6	1.5239	0.3083	-0.138	2.1337	0.5123	1.7166	-0.0808	0.2192	0.1132	-0.2809	0.0555	0.2867	-0.3401	-0.0575	0.0173	0.3753	-0.0514	0.0438	0.3281	0.0204	0.3778	27.8833	53.1498	32.1375
7	9.456	1.3793	-5.7478	3.3053	-1.0771	7.966	-0.1526	0.1113	-0.1463	-0.2444	0.0986	0.0654	-0.0368	0.193	0.1049	0.3669	-0.0578	0.012	0.1976	-0.0234	0.2542	36.5806	52.8126	38.7379
8	6.4387	2.4983	6.9447	6.5372	2.3353	9.8311	-0.5662	-0.7718	0.6999	-0.0924	0.1153	0.5143	-1.0677	-0.6015	0.4575	0.5855	-0.021	0.1851	0.3552	-0.0152	0.4004	29.6667	62.4762	39.6049
9	0.7365	-0.5196	1.7242	1.0502	-1.2544	2.0934	0.0047	0.3536	0.1239	-0.0168	0.2467	-0.2521	-1.5219	1.1798	-0.3399	1.0057	-0.3019	0.2712	0.7821	-0.1164	0.5339	50.4166	51.6024	2.8063
10	1.6097	-0.3627	1.3416	3.2912	-2.617	5.9085	0.014	-0.1986	0.324	0.2589	0.3011	-0.0089	-2.0469	-0.0205	-0.3005	1.1665	-0.185	0.3081	0.5143	-0.1005	0.5023	44.7727	53.5604	2.6019
11	4.7938	-0.0838	0.1946	5.5798	-2.5705	1.2801	0.6611	-0.4008	0.323	-0.6484	0.1147	-0.3899	-0.9954	0.0309	-0.7614	0.9175	-0.0294	0.292	0.5156	-0.0439	0.4855	41.2844	48.4126	-2.4181
12	2.8014	0.6167	1.6585	1.2639	0.0892	4.132	0.1235	0.2466	0.1872	0.0635	0.2966	-0.2445	-0.9159	1.108	-0.419	0.5113	-0.1757	0.2059	0.6076	-0.1975	0.4598	52.3305	41.4048	-0.268
13	1.3285	0.4373	0.7679	2.1343	1.0169	6.106	0.4318	0.0529	0.2567	0.0137	0.1881	-0.1046	-1.4929	0.1635	-0.5754	0.8854	-0.0522	0.2649	0.3589	0.046	0.4004	42.4106	48.9837	-7.125
14	3.7407	0.1797	0.98	1.6685	0.4518	2.1893	0.9829	0.7497	-0.1541	-0.0961	-0.0722	-0.2631	-0.7446	0.1438	-0.8186	0.3445	0.0663	0.1727	0.5323	-0.0247	0.4443	42.964	36.132	-2.0684
15	7.6453	-3.7614	0.4617	6.7393	1.6099	6.2791	0.7279	0.0732	-0.4816	-0.1321	-0.0842	0.5045	-0.5937	-0.4196	-0.646	0.348	0.0408	0.0604	0.3493	0.0898	0.2944	37.6333	36.492	-3.6404
16	7.7529	3.5248	2.984	6.3497	-0.3591	4.0385	0.6217	0.8405	-0.8515	-0.3282	0.23	-0.4112	-0.417	0.7579	-0.8269	0.4195	-0.0654	0.1206	0.4116	-0.1261	0.3134	45.9849	36.4602	-6.163
17	9.6509	6.2928	-5.3778	2.0244	-6.7526	5.265	0.0546	-0.765	-0.5546	-0.9107	0.0759	-1.247	-0.1104	1.6189	-0.0167	0.646	-0.106	0.0723	1.0241	-0.3093	0.6272	63.4622	33.9586	1.9482
18	5.8861	-5.6303	0.6422	7.2456	0.4604	6.755	0.1806	0.1479	0.8073	0.5931	0.1382	-0.2816	-0.9607	-0.3891	-0.3049	0.413	0.0259	0.2017	0.4772	0.0608	0.5336	39.5318	42.2118	6.0769
19	6.3708	-5.367	1.2226	9.8148	-1.4557	8.009	0.3501	-0.0055	0.1374	0.3373	-0.2047	-0.082	-0.26	-0.7493	-0.236	0.4188	-0.1299	0.1141	0.5331	-0.0759	0.2897	41.4173	40.0021	7.6334
20	3.5605	-3.8788	-1.8003	6.2318	2.9267	2.4937	-0.1288	-0.6124	-0.1675	1.0853	0.2331	0.2464	0.3779	0.3491	-0.0666	0.8372	-0.1145	0.1475	0.5548	0.0394	0.3885	41.2801	27.282	74.7218
21	2.1835	-1.9499	1.0111	5.7833	-1.9008	0.7719	0.2828	-0.4701	0.1366	0.453	-0.1441	-0.1531	-0.0623	0.1319	-0.0949	0.8741	-0.0903	0.1855	0.5482	0.0345	0.3941	36.1769	26.2375	71.4032
22	2.1261	-0.5687	-0.2765	1.9551	0.4788	1.7508	0.0607	-0.2534	-0.0579	0.3562	-0.0977	-0.0707	0.2125	0.3638	0.0407	0.5481	-0.048	0.1025	0.4605	0.0172	0.2744	45.8895	25.7396	62.985
23	4.1046	-0.4978	-1.2306	2.3271	1.3119	2.4431	0.1174	-0.0755	-0.1162	0.4852	-0.0868	0.2186	0.0469	-0.2021	-0.0058	0.5505	-0.0507	0.1457	0.298	0.0442	0.2783	35.036	30.1263	61.9251
24	2.0189	0.0872	0.6233	0.3383	-0.0113	1.6107	0.0041	0.7224	0.1158	0.1661	-0.0787	0.1655	-0.058	0.2863	0.0962	0.5112	-0.0829	0.1469	0.395	0.003	0.3567	40.0147	30.9514	56.5506
25	2.0393	6.325	9.7383	7.9622	4.8067	2.0564	-0.2836	0.019	-0.9681	-0.3231	0.8342	-0.895	-1.0272	0.9961	-0.5141	0.625	-0.0311	0.1233	0.8316	-0.1388	0.4392	57.1054	21.7314	56.4675
26	1.9815	-5.0474	1.9582	7.9241	7.7339	1.992	-0.9014	-0.1052	-0.5025	0.7868	-0.0065	0.8027	2.4769	-0.9022	0.9296	0.7449	-0.1357	0.1144	0.4493	-0.0303	0.4546	32.8444	20.2378	64.6976
27	9.6023	-6.0692	-7.378	7.8639	6.3648	8.1768	-0.5548	-0.616	-0.3767	0.8472	0.3965	0.6705	1.2791	-0.0216	0.2253	0.6589	-0.0957	0.1023	0.4687	0.0671	0.4151	34.5625	19.9895	66.2168
28	2.2785	-1.0383	-0.5397	2.6203	-0.4191	1.402	-0.0734	-0.3307	0.3241	0.7228	0.0743	-0.0543	-0.5998	0.2277	-0.0021	0.7375	-0.1443	0.0791	0.4978	-0.0599	0.3435	45.0318	54.8803	65.6495
29	6.0419	-2.1498	-1.4098	3.2807	0.3218	3.545	-0.0143	-0.1513	0.2125	0.3449	0.0552	0.2535	-0.5527	0.1697	-0.0701	0.5851	-0.0954	0.1069	0.2809	-0.0545	0.3129	38.359	55.5365	56.5854
30	9.0493	-3.9078	7.4483	6.5547	-4.721	9.4753	0.1236	1.1901	-0.0227	-0.0759	-0.2821	-0.3543	-1.2278	1.9274	0.1915	0.9259	-0.2638	0.2067	0.8573	-0.146	0.4748	48.6938	61.7142	59.0214
31	1.8887	1.7127	-1.3612	2.855	-3.1787	4.222	0.5037	-0.1397	-0.3786	0.3388	0.2297	0.2658	1.4522	-0.2672	-0.5178	1.5265	-0.2879	-0.486	0.5401	0.2155	0.7995	32.1453	6.1467	-2.8417
32	0.4105	-0.1091	-0.6321	0.1355	0.5814	2.5219	-0.0807	-0.1802	-1.0302	-0.0254	0.2209	0.0299	1.7307	0.3146	-0.3328	1.8904	-0.032	-0.5951	0.3477	0.1071	0.6976	37.48	4.6495	-1.9241
33	7.511	0.283	-0.4619	2.7049	-0.1404	0.035	0.8225	-0.0441	-0.1536	-0.4003	-0.2311	-0.1428	1.1861	0.2399	-0.5828	1.1748	0.158	-0.3778	0.4766	-0.0338	0.6018	41.397	8.7384	-7.8851
34	0.3019	-0.0216	0.3458	1.2666	0.0965	4.3478	0.3657	-0.0991	-0.2814	-0.0878	0.3391	0.1549	1.8221	-0.2325	-0.6024	0.8817	-0.1067	-0.3483	0.415	0.0805	0.5402	33.6551	14.7208	-6.0533
35	3.5061	-2.0263	-1.4255	4.3305	-0.0029	4.4047	0.6755	0.0148	-0.1601	-0.088	0.0562	-0.1433	0.9461	0.3635	-0.6329	0.4575	0.0706	-0.1819	0.3552	-0.066	0.3629	42.157	22.1483	-4.4798
36	8.7114	1.4899	-0.9166	4.1481	0.5837	4.9701	0.5975	0.0025	-0.1675	-0.1936	0.2872	0.0643	0.768	-0.3395	-0.863	0.5351	-0.0235	-0.2066	0.335	0.0443	0.3865	36.7862	22.7841	-7.8384
37	2.6803	0.2987	-1.713	9.2962	3.0631	6.0625	-0.0859	-0.5781	-0.2388	0.3026	0.5883	-0.3351	0.9879	-0.238	-0.4585	0.6394	-0.2054	-0.1942	0.3762	0.2264	0.3613	33.1088	17.1465	0.9575
38	2.2834	0.2921	-1.369	0.0361	-0.2236	0.8158	0.4908	0.3084	-0.9616	0.2417	-0.3538	-0.0175	1.878	0.5373	-0.1083	1.2467	0.2424	-0.369	0.5599	-0.0657	0.6516	41.2586	11.2509	3.2119
39	3.5528	4.4471	2.9296	9.8639	3.5936	2.4087	0.1346	-1.0028	0.4087	1.8798	-0.0552	1.0166	-0.3918	-0.6821	-0.1973	0.7221	-0.0198	0.1452	0.5499	-0.031	0.3617	35.6796	36.8357	12.9177
40	1.8889	1.5474	-1.0149	1.9752	-1.2014	2.2425	-0.3359	0.6078	-0.5246	-0.5701	0.4321	-0.3021	2.073	-0.6999	-0.0885	1.4073	-0.2547	-0.4318	0.6896	0.0638	0.6527	31.694	10.2291	-36.2376
41	1.3478	0.3388	-0.8754	1.5281	-0.5881	2.8697	0.0016	0.3969	-0.3922	-0.6375	0.3868	0.4097	1.2658	-0.7458	-0.3982	0.9653	-0.3269	-0.3396	0.7983	0.154	0.6796	26.9502	15.485	-33.3642
42	2.9903	-0.1375	-1.2226	2.6282	0.5188	5.3889	0.1047	0.495	-0.3203	-0.4318	0.5427	-0.0107	1.4074	-0.2868	-0.631	0.7413	-0.0751	-0.2736	0.5209	-0.0091	0.4955	36.5104	16.5213	-31.123
43	0.5773	0.841	-0.8498	3.4573	1.3517	4.4362	-0.1643	-0.5481	0.082	-0.427	1.0793	-0.2237	0.3939	0.3069	-0.8391	0.4167	0.0349	-0.093	0.5908	0.0026	0.3965	37.7531	26.4055	-31.3479
44	4.529	0.1724	-1.847	5.3082	2.629	7.502	-0.1681	0.0724	0.0071	-0.1125	0.8682	0.7344	-0.0947	-0.2711	-0.7134	0.3846	-0.0444	-0.056	0.4245	0.1576	0.4654	33.8341	29.8251	-29.431
45	3.2702	0.6314	-1.9212	4.9476	0.1136	6.5222	-0.4008	0.1444	-0.253	-0.1234	0.8063	-0.6664	1.4893	1.158	-0.3882	0.7298	0.062	-0.1795	0.6686	-0.2011	0.4536	46.3107	18.7276	-32.1622
46	5.059	4.6252	-5.8996	6.5025	-3.3961	8.383	-0.5702	2.0758	0.5779	-0.8819	1.4601	1.1259	0.278	-1.1137	-0.8019	0.8222	-0.1216	-0.2871	0.6721	0.039	0.7185	30.3402	24.6509	-38.195
47	9.5827	2.1731	-7.383	4.246	-1.1042	6.7114	-0.1187	0.4388	0.2359	-1.3029	0.5437	0.6104	0.4086	-1.0303	-0.3733	1.0056	-0.2392	-0.4034	0.8457	0.1318	0.788	32.8524	22.9771	-40.7761
48	0.5933	0.2689	-1.1552	0.9328	-0.9101	2.9925	0.2748	0.3256	0.1237	-0.3866	1.2943	-0.5304	-1.4588	1.6702	-0.5197	1.3375	-0.8474	0.7699	1.0933	-0.2298	0.3584	54.55	51.3774	-29.3847
49	2.2259	-0.4044	2.3782	1.4284	-1.3758	3.811	-0.062	0.2534	-0.132	-0.343	0.6995	0.1695	-1.6271	0.2533	-0.6232	1.0757	-0.0976	0.2953	0.5113	-0.0506	0.4903	39.9437	49.869	-32.7325
50	1.328	0.9887	0.8211	0.8878	0.4466	3.4165	0.2382	0.1317	0.0241	-0.2672	0.5127	-0.1191	-1.0327	0.9787	-0.7018	0.683	-0.1915	0.2835	0.7054	-0.2029	0.5354	49.3174	44.1052	-25.1195
51	2.2616	1.7348	0.229	1.5551	-0.8393	5.4866	-0.0665	0.0861	-0.0516	0.1596	0.7156	-0.9945	0.0452	1.0705	-0.6295	0.4409	-0.1088	0.1206	0.6419	-0.3169	0.6643	49.0316	34.8818	-28.8021
52	4.6394	-3.714	3.2896	4.7215	-2.1739	4.4176	0.483	0.0758	-0.116	-0.6026	0.2818	0.1113	-0.994	0.4385	-0.7414	0.6034	-0.1331	0.2013	0.496	-0.0521	0.3791	42.9469	40.1305	-25.5592
53	5.5371	2.3127	2.4595	3.8449	-0.3546	5.1725	0.0234	0.7527	-0.185	-0.203	0.422	-0.1402	-1.103	0.5046	-0.4209	1.0058	-0.1899	0.2312	0.5034	-0.0263	0.3351	44.1635	47.2498	-33.7601
54	3.5907	-3.1169	1.9192	4.4377	-3.0508	3.1002	0.1381	0.5709	0.5472	-1.2059	-0.1558	-0.1379	-0.2963	1.2391	0.0281	0.9908	-0.2762	0.3555	0.9794	-0.2346	0.6325	49.9167	44.3603	-38.256

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 2:33)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 34:152)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 153:180)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 181:205)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 206:222)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 3:152)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 153:192)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 193:230)
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESID 3:21)
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESID 22:47)
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESID 48:68)
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESID 69:111)
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESID 112:134)
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 135:152)
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESID 153:168)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESID 169:180)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESID 181:192)
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESID 193:205)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESID 206:226)
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESID 3:33)
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESID 34:68)
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESID 69:111)
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 112:168)
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESID 169:180)
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESID 181:192)
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESID 193:205)
27	X-RAY DIFFRACTION	27	CHAIN D AND (RESID 206:222)
28	X-RAY DIFFRACTION	28	CHAIN E AND (RESID 3:134)
29	X-RAY DIFFRACTION	29	CHAIN E AND (RESID 135:203)
30	X-RAY DIFFRACTION	30	CHAIN E AND (RESID 204:222)
31	X-RAY DIFFRACTION	31	CHAIN F AND (RESID 3:21)
32	X-RAY DIFFRACTION	32	CHAIN F AND (RESID 22:44)
33	X-RAY DIFFRACTION	33	CHAIN F AND (RESID 45:68)
34	X-RAY DIFFRACTION	34	CHAIN F AND (RESID 69:134)
35	X-RAY DIFFRACTION	35	CHAIN F AND (RESID 135:168)
36	X-RAY DIFFRACTION	36	CHAIN F AND (RESID 169:180)
37	X-RAY DIFFRACTION	37	CHAIN F AND (RESID 181:208)
38	X-RAY DIFFRACTION	38	CHAIN F AND (RESID 209:219)
39	X-RAY DIFFRACTION	39	CHAIN F AND (RESID 220:230)
40	X-RAY DIFFRACTION	40	CHAIN G AND (RESID 3:21)
41	X-RAY DIFFRACTION	41	CHAIN G AND (RESID 22:68)
42	X-RAY DIFFRACTION	42	CHAIN G AND (RESID 69:134)
43	X-RAY DIFFRACTION	43	CHAIN G AND (RESID 135:152)
44	X-RAY DIFFRACTION	44	CHAIN G AND (RESID 153:168)
45	X-RAY DIFFRACTION	45	CHAIN G AND (RESID 169:192)
46	X-RAY DIFFRACTION	46	CHAIN G AND (RESID 193:208)
47	X-RAY DIFFRACTION	47	CHAIN G AND (RESID 209:221)
48	X-RAY DIFFRACTION	48	CHAIN H AND (RESID 3:68)
49	X-RAY DIFFRACTION	49	CHAIN H AND (RESID 69:96)
50	X-RAY DIFFRACTION	50	CHAIN H AND (RESID 97:152)
51	X-RAY DIFFRACTION	51	CHAIN H AND (RESID 153:168)
52	X-RAY DIFFRACTION	52	CHAIN H AND (RESID 169:180)
53	X-RAY DIFFRACTION	53	CHAIN H AND (RESID 181:208)
54	X-RAY DIFFRACTION	54	CHAIN H AND (RESID 209:221)

-
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