PDB-8ifj: Crystal structure of pyrrolysyl-tRNA synthetase from methanogenic...

ID or keywords:

Entry

Database: PDB / ID: 8ifj

Title

Crystal structure of pyrrolysyl-tRNA synthetase from methanogenic archaeon ISO4-G1

Components

Pyrrolysyl-tRNA synthetase PylS

Keywords

TRANSLATION /

non-canonical amino acids /

genetic code expansion /

tRNA

Function / homology

Function and homology information

tRNA aminoacylation / aminoacyl-tRNA ligase activity /

tRNA binding /

translation /

Biological species

methanogenic archaeon mixed culture ISO4-G1 (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.78 Å

Authors

Yanagisawa, T. / Tanabe, H. / Yokoyama, S.

Funding support

Japan, 4items

Organization	Grant number	Country
Japan Agency for Medical Research and Development (AMED)	JP17am0101081	Japan
Japan Agency for Medical Research and Development (AMED)	JP19gm0010001	Japan
Japan Society for the Promotion of Science (JSPS)	16K05859	Japan
Japan Society for the Promotion of Science (JSPS)	24550203	Japan

Citation

Journal: Int J Mol Sci / Year: 2023
Title: Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids.
Authors: Yanagisawa, T. / Seki, E. / Tanabe, H. / Fujii, Y. / Sakamoto, K. / Yokoyama, S.

History

Deposition	Feb 18, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2023	Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ifj.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8ifj.ent.gz	922.3 KB	Display	PDB format
PDBx/mmJSON format	8ifj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/if/8ifj ftp://data.pdbj.org/pub/pdb/validation_reports/if/8ifj	HTTPS FTP

-
Related structure data

Similar structure data	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	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (4)

Deposited unit

A: Pyrrolysyl-tRNA synthetase PylS

B: Pyrrolysyl-tRNA synthetase PylS

C: Pyrrolysyl-tRNA synthetase PylS

D: Pyrrolysyl-tRNA synthetase PylS

E: Pyrrolysyl-tRNA synthetase PylS

F: Pyrrolysyl-tRNA synthetase PylS

G: Pyrrolysyl-tRNA synthetase PylS

H: Pyrrolysyl-tRNA synthetase PylS

I: Pyrrolysyl-tRNA synthetase PylS

J: Pyrrolysyl-tRNA synthetase PylS

313 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyrrolysyl-tRNA synthetase PylS

B: Pyrrolysyl-tRNA synthetase PylS

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

2

C: Pyrrolysyl-tRNA synthetase PylS

G: Pyrrolysyl-tRNA synthetase PylS

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

3

D: Pyrrolysyl-tRNA synthetase PylS

F: Pyrrolysyl-tRNA synthetase PylS

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

4

E: Pyrrolysyl-tRNA synthetase PylS

H: Pyrrolysyl-tRNA synthetase PylS

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

5

I: Pyrrolysyl-tRNA synthetase PylS

J: Pyrrolysyl-tRNA synthetase PylS

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

Unit cell

Length a, b, c (Å)	98.510, 102.680, 349.860
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pyrrolysyl-tRNA synthetase PylS Mass: 31256.469 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) methanogenic archaeon mixed culture ISO4-G1 (environmental samples) Gene: AUP07_0651 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A126QV54
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.83 Å³/Da / Density % sol: 56.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7.2 / Details: HEPES, PEG 3350, KCl

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL32XU / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.78→49.867 Å / Num. obs: 172270 / % possible obs: 99.9 % / Redundancy: 5.988 % / B_iso Wilson estimate: 78.526 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.145 / R_rim(I) all: 0.159 / Χ²: 1.125 / Net I/σ(I): 9.77 / Num. measured all: 1031551 / Scaling rejects: 7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.78-2.85	6.066	1.866	1.01	77389	12770	12757	0.692	2.042	99.9
2.85-2.93	6.094	1.515	1.27	75597	12425	12405	0.768	1.657	99.8
2.93-3.02	5.994	1.121	1.74	72317	12076	12064	0.863	1.229	99.9
3.02-3.11	5.914	0.925	2.12	69522	11769	11755	0.895	1.015	99.9
3.11-3.21	5.786	0.684	2.88	65988	11413	11405	0.935	0.752	99.9
3.21-3.32	5.579	0.512	3.79	61211	10982	10971	0.954	0.564	99.9
3.32-3.45	5.103	0.417	4.61	54150	10629	10611	0.95	0.464	99.8
3.45-3.59	5.219	0.303	6.23	53052	10197	10166	0.982	0.337	99.7
3.59-3.75	5.773	0.259	8.17	56821	9851	9842	0.986	0.285	99.9
3.75-3.93	5.485	0.205	10.17	51397	9380	9370	0.992	0.226	99.9
3.93-4.14	5.496	0.152	12.74	48950	8907	8906	0.995	0.167	100
4.14-4.4	6.366	0.138	15.94	53510	8409	8405	0.997	0.15	100
4.4-4.7	6.474	0.121	18.7	51226	7913	7913	0.997	0.131	100
4.7-5.08	6.431	0.1	21.08	47612	7404	7404	0.997	0.109	100
5.08-5.56	6.646	0.112	19.63	44912	6760	6758	0.997	0.122	100
5.56-6.22	6.693	0.106	21.49	41077	6137	6137	0.997	0.115	100
6.22-7.18	6.921	0.102	23.53	37465	5415	5413	0.997	0.11	100
7.18-8.79	7.148	0.085	27.83	32660	4569	4569	0.997	0.092	100
8.79-12.43	6.881	0.055	32.51	24214	3519	3519	0.998	0.06	100
12.43-49.867	6.569	0.052	32.57	12481	1935	1900	0.998	0.056	98.2

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.16_3549	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.78→49.867 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2962	3798	2.21 %
R_work	0.2326	168163	-
obs	0.234	171961	99.72 %

Solvent computation

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

Displacement parameters

B_iso max: 223.18 Å² / B_iso mean: 100.0042 Å² / B_iso min: 27.71 Å²

Refinement step

Cycle: final / Resolution: 2.78→49.867 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21566	0	0	49	21615
B_iso mean	-	-	-	57.18	-
Num. residues	-	-	-	-	2712

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.78-2.8152	0.4103	132	0.405	6224	100
2.8152-2.8522	0.442	133	0.3986	6247	100
2.8522-2.8913	0.5284	158	0.3903	6183	100
2.8913-2.9326	0.3335	148	0.3763	6214	100
2.9326-2.9763	0.401	124	0.3424	6233	99
2.9763-3.0228	0.3565	147	0.3145	6229	100
3.0228-3.0724	0.3178	141	0.3155	6213	100
3.0724-3.1254	0.3676	140	0.3044	6199	100
3.1254-3.1822	0.3906	118	0.3048	6242	100
3.1822-3.2434	0.35	152	0.3076	6237	100
3.2434-3.3096	0.4284	146	0.3034	6258	100
3.3096-3.3815	0.3528	153	0.3105	6162	100
3.3815-3.4602	0.2923	126	0.2851	6232	100
3.4602-3.5467	0.3633	136	0.2687	6243	100
3.5467-3.6425	0.3659	155	0.2557	6249	100
3.6425-3.7497	0.301	131	0.2468	6219	100
3.7497-3.8707	0.2695	136	0.2386	6185	100
3.8707-4.009	0.2596	147	0.2239	6232	100
4.009-4.1694	0.2821	140	0.2173	6257	100
4.1694-4.359	0.2652	131	0.2081	6261	100
4.359-4.5887	0.2472	141	0.1935	6219	100
4.5887-4.876	0.2172	139	0.1811	6286	100
4.876-5.2521	0.2425	148	0.1785	6210	100
5.2521-5.7799	0.2721	146	0.2152	6234	100
5.7799-6.6146	0.2971	138	0.2132	6261	100
6.6146-8.3274	0.2824	150	0.2159	6237	100
8.3274-49.867	0.2809	142	0.1764	6197	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	0.8801	0.4851	-1.7897	1.1623	-2.2853	8.4127	-0.3127	0.3712	-0.0192	-0.3593	0.1954	0.1552	1.0903	-0.9304	0.1281	0.5136	-0.0577	-0.0236	0.7557	0.0908	0.6244	38.2987	7.7712	-60.7771
2	8.2725	-0.4207	-5.1436	2.6439	-0.9684	6.8967	-0.1969	-0.2074	-0.5719	0.189	-0.06	-0.0541	0.8577	0.1636	0.2171	0.4422	-0.0063	-0.1364	0.3048	0.0075	0.495	46.4049	-2.1635	-29.5995
3	2.3256	1.7475	-0.8095	4.3311	-3.4921	7.8712	-0.0656	0.1433	-0.2144	-0.5075	0.4921	0.3195	1.5673	-1.2976	-0.4284	0.6447	-0.1456	-0.0861	0.6372	0.0622	0.5494	34.1217	-5.1617	-37.4941
4	1.3788	0.3612	1.1533	0.4496	-0.581	6.2554	0.0848	0.4025	0.6611	0.7487	-0.3893	-0.7132	-1.409	-0.2048	0.1502	1.5782	0.0352	-0.2598	0.6939	0.003	0.9115	49.6782	17.1163	-0.0891
5	1.0775	-0.0414	0.489	2.0016	-1.4534	6.5657	-0.1046	0.1026	0.1225	0.3962	0.1224	-0.1487	-0.6047	-0.2795	0.0199	0.3602	0.0332	-0.052	0.275	0.0053	0.5202	46.8209	15.9521	-30.3237
6	2.1715	-0.2718	-1.6854	3.7236	-1.9747	7.071	-0.1024	-0.2521	0.3119	0.2574	0.1156	-0.2628	-0.5547	0.1154	0.1676	0.4338	0.0035	0.0398	0.337	-0.06	0.6242	49.7215	19.1232	-33.8843
7	2.1441	-0.1601	-0.4029	4.4674	-1.3001	6.9585	-0.0559	-0.3861	1.0499	0.6036	0.1841	0.0007	-1.9951	-0.0203	-0.1533	1.1212	0.104	-0.0253	0.6221	-0.0445	0.87	44.1189	33.4474	-33.9968
8	5.2688	-0.3384	-4.0113	4.3685	-1.5136	3.7421	0.0409	-1.3539	0.6539	0.5652	0.394	-0.1934	-1.9293	1.6595	-0.0796	0.9737	-0.1487	-0.0333	0.6748	-0.0027	0.8301	52.6727	32.6661	-37.3138
9	0.9051	-0.0207	-0.1587	4.8093	-2.0706	7.0469	-0.0163	0.0653	0.4231	0.6771	0.2628	-0.0624	-0.8878	-0.2225	-0.0969	0.4019	0.0654	0.0132	0.4005	0.0273	0.5771	45.2134	19.5319	-27.0492
10	2.0633	0.3291	-0.2536	1.6145	-0.7174	4.8525	0.3728	0.1211	-0.1184	0.0229	-0.2569	-0.1224	0.3247	0.7728	-0.0908	0.6152	0.0249	-0.0354	0.6953	0.0075	0.5532	2.9969	53.7286	-26.4983
11	3.0408	2.1441	-1.0299	4.6763	-2.4025	6.475	0.3692	0.3048	0.2893	0.2603	-0.3361	-0.4425	-0.3416	1.203	-0.0552	0.5947	-0.0635	0.03	0.8279	0.0353	0.5854	8.1003	62.4519	-31.7939
12	2.9137	-1.0144	-1.2787	3.2646	0.8257	8.9605	0.0031	0.2377	-0.6082	-0.6503	0.3445	0.0154	1.213	-0.0174	-0.0958	1.544	0.3573	-0.2754	1.0092	-0.0689	0.8458	34.2413	49.5372	-36.4355
13	1.944	-0.8949	-0.2686	1.461	-1.2573	6.3114	0.0902	0.129	-0.2804	-0.2704	0.0257	0.2001	0.7697	-0.1013	-0.1528	0.8829	0.0086	-0.1371	0.2767	0.079	0.7701	35.9776	52.1513	-9.3058
14	1.2755	-0.1198	-0.5006	1.4141	-0.9814	5.3667	-0.0275	-0.6955	-0.5322	0.2891	0.0555	0.5465	1.0443	-0.0599	0.2297	0.883	0.0235	-0.1218	0.4758	0.1588	0.9627	37.9586	45.1101	9.7434
15	4.2444	2.3306	-0.3672	5.9671	-1.9212	4.6524	-0.052	1.3508	-1.0703	-0.2678	0.3301	0.0022	1.316	-1.0035	0.0628	1.2781	-0.2259	-0.2877	0.5061	-0.0445	0.9484	32.2875	40.9165	-1.504
16	2.5493	0.2512	-1.6731	3.5285	0.4471	1.8109	0.3634	0.1866	-0.7975	-1.7019	0.0373	0.0894	2.1074	0.5717	0.0337	2.0825	-0.2752	-0.231	1.1765	-0.1763	1.3812	29.6709	31.5493	-6.2965
17	0.8339	1.4653	0.6406	2.6011	0.5438	7.2468	0.7482	-0.173	-1.7116	0.3368	0.7605	-0.1618	2.712	0.8991	0.5125	2.2817	0.24	-0.1434	0.7322	0.2089	1.1929	40.4692	32.4681	11.2484
18	2.3984	1.2522	-1.2973	3.269	-1.2133	3.5334	0.0876	0.7491	-0.6792	-0.8957	0.5599	0.3093	1.7715	-0.2548	-0.2366	1.4092	-0.0102	-0.4475	0.5525	0.0785	0.9237	32.0724	50.9874	-13.1264
19	2.3654	-0.1006	-0.1513	1.1301	-0.3324	4.7437	0.0754	0.2712	-0.1341	0.312	0.0971	-0.0511	0.2931	0.9245	-0.2015	0.6021	0.0629	-0.0671	0.9086	0.0155	0.6641	2.5609	3.0848	-54.8892
20	3.4235	1.932	-4.2736	7.5772	-3.5402	6.9265	-0.1979	0.3651	0.2183	-0.1253	0.3153	-0.5464	0.6003	1.3238	0.1493	0.4293	0.0241	-0.0576	1.5439	-0.0731	0.6498	7.2163	4.5191	-74.9786
21	3.3406	0.3031	-0.8533	1.2235	0.3029	3.1418	-0.079	0.5017	0.343	0.1038	0.2894	-0.3468	-0.1416	1.8103	-0.2006	0.5199	-0.0755	-0.0225	1.5522	-0.0017	0.61	10.3912	12.5926	-66.7589
22	1.4837	-0.0578	0.0242	2.0465	-1.494	7.0299	-0.014	-0.2005	0.0489	0.5825	0.0327	0.059	-0.5588	0.2535	-0.0578	0.9433	-0.0025	0.0216	0.3361	0.068	0.7264	40.976	62.7306	13.6939
23	0.8295	-0.9214	0.3648	4.7499	-3.0845	4.3947	-0.0199	-0.046	0.2092	0.9502	0.1124	0.1213	-1.1901	0.0106	-0.0502	1.2036	0.0917	0.0403	0.5586	0.0673	0.6585	35.6503	73.0397	1.0026
24	5.3056	0.4731	-2.9425	9.9402	6.1391	6.4152	-0.4777	0.1439	-0.7133	0.4246	0.2752	0.0451	0.6917	-1.0592	0.2125	1.1801	-0.0482	-0.2112	1.5814	0.0783	0.7713	-8.7851	43.0621	-70.2225
25	2.9632	0.174	-0.6497	1.0666	0.0033	3.9592	0.401	0.6731	-0.3968	-0.1715	-0.0542	0.0802	0.8531	-0.2128	-0.2256	0.791	-0.0245	-0.1771	0.5853	-0.0773	0.5614	-8.198	45.2814	-39.7575
26	8.1683	0.0744	-1.8348	3.2834	-2.9802	3.0404	0.5532	0.2217	-0.6306	-0.8591	-0.3501	0.2407	0.7948	0.0399	-0.153	0.892	-0.063	-0.3167	0.5861	0.0111	0.6979	-10.1069	41.2356	-36.2304
27	5.1021	1.3466	0.0916	1.7004	-1.096	4.427	0.2691	0.6862	-0.5498	-0.2105	0.1822	0.2616	1.4261	-1.1067	-0.3676	1.0959	-0.2747	-0.2075	0.8942	0.0337	0.7333	-19.769	42.6677	-38.337
28	3.9152	1.4628	4.1443	1.5491	1.8415	4.5577	0.1729	0.8362	-0.4241	0.2636	-0.0035	0.6112	0.5591	-0.0505	-0.1612	1.3439	-0.381	-0.0137	2.0684	0.0877	0.8202	-10.4977	-4.8654	-102.9183
29	2.6617	0.3845	-0.4631	2.1378	-0.1967	6.9739	0.0399	0.6504	-0.1525	0.1132	0.0076	0.0715	0.9445	-0.0973	0.001	0.4012	-0.0817	-0.0795	0.9327	0.0635	0.5374	-10.0503	-1.5831	-72.8722
30	5.1298	-1.3433	-2.5272	3.9283	1.153	4.7524	0.1292	0.3122	-0.3663	-0.4467	-0.2276	0.5303	-0.0706	0.1587	0.1155	0.576	-0.0814	-0.1458	1.0926	0.1966	0.697	-12.8993	-4.7894	-69.6122
31	5.1472	0.2352	-0.969	2.2337	1.0435	6.5047	-0.0617	0.7869	-0.3309	0.0113	-0.1697	0.4868	0.4814	-0.8859	0.0558	0.5244	-0.1284	-0.0583	1.0833	0.1171	0.6662	-21.9903	-0.7091	-71.764
32	2.8473	-0.4938	-0.4408	1.1232	-0.0679	6.1995	-0.0505	-0.5674	-0.174	0.2769	0.1265	0.3313	0.1907	-0.3976	-0.0968	0.3951	-0.0502	0.1425	0.7569	0.0329	0.689	41.1667	66.8495	-81.3356
33	3.7179	-0.8525	-0.5472	1.612	-0.4498	5.6231	-0.2905	-0.5721	-0.1275	0.5251	0.3267	0.7914	-0.1997	-1.671	0.0869	0.6032	0.0861	0.2197	1.2999	0.0764	0.8004	32.956	72.3477	-73.2115
34	7.9524	-2.1057	6.447	6.3348	-3.6204	5.8324	-0.4362	0.7021	-1.7817	0.2002	1.6516	0.1857	-2.2066	-1.3879	-0.9342	1.5615	0.3479	0.2262	2.2357	-0.0294	1.0185	52.9053	61.33	-37.7175
35	2.6379	0.6285	0.18	2.2001	-0.0136	4.7347	-0.0715	-0.8663	-0.0931	0.5951	0.2466	0.0257	0.3562	0.4793	-0.0275	0.5605	0.1416	0.0324	1.0631	-0.045	0.5149	54.4807	64.5605	-66.2621
36	7.9405	3.8256	-3.7173	7.4144	-3.7393	3.0245	-0.0293	-0.9034	-0.5358	1.1814	0.2772	-0.0825	-0.4139	0.4855	0.0893	0.7756	0.0322	-0.0087	1.2531	-0.0878	0.6152	58.0274	61.9357	-69.1934
37	5.1167	-0.9295	1.4215	2.4378	0.0215	2.7368	0.0176	-0.521	0.3927	0.3213	0.0685	-0.444	0.0482	1.8287	-0.1733	0.7485	0.0293	-0.0039	1.895	-0.2036	0.7259	71.6781	67.7072	-71.7189
38	5.0446	-0.3338	2.0904	1.5455	-0.3073	2.7517	0.0721	-2.5355	0.1717	0.5434	0.3389	0.0582	-0.1128	1.2056	-0.2417	0.8872	0.2375	0.0692	1.8684	-0.1603	0.6651	54.9124	67.7264	-56.9913

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 75 )	A	2 - 75
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 76 through 159 )	A	76 - 159
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 160 through 273 )	A	160 - 273
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 28 )	B	2 - 28
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 29 through 134 )	B	29 - 134
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 135 through 159 )	B	135 - 159
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 160 through 214 )	B	160 - 214
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 215 through 228 )	B	215 - 228
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 229 through 273 )	B	229 - 273
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 148 )	C	2 - 148
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 149 through 273 )	C	149 - 273
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 28 )	D	1 - 28
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 29 through 113 )	D	29 - 113
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 114 through 148 )	D	114 - 148
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 149 through 189 )	D	149 - 189
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 190 through 219 )	D	190 - 219
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 220 through 236 )	D	220 - 236
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 237 through 273 )	D	237 - 273
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1 through 120 )	E	1 - 120
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 121 through 159 )	E	121 - 159
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 160 through 273 )	E	160 - 273
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 1 through 120 )	F	1 - 120
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 121 through 273 )	F	121 - 273
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 2 through 28 )	G	2 - 28
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 29 through 134 )	G	29 - 134
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 135 through 159 )	G	135 - 159
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 160 through 273 )	G	160 - 273
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 3 through 30 )	H	3 - 30
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 31 through 134 )	H	31 - 134
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 135 through 159 )	H	135 - 159
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 160 through 273 )	H	160 - 273
32	X-RAY DIFFRACTION	32	chain 'I' and (resid 1 through 134 )	I	1 - 134
33	X-RAY DIFFRACTION	33	chain 'I' and (resid 135 through 273 )	I	135 - 273
34	X-RAY DIFFRACTION	34	chain 'J' and (resid 5 through 30 )	J	5 - 30
35	X-RAY DIFFRACTION	35	chain 'J' and (resid 31 through 134 )	J	31 - 134
36	X-RAY DIFFRACTION	36	chain 'J' and (resid 135 through 159 )	J	135 - 159
37	X-RAY DIFFRACTION	37	chain 'J' and (resid 160 through 236 )	J	160 - 236
38	X-RAY DIFFRACTION	38	chain 'J' and (resid 237 through 273 )	J	237 - 273

-
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