PDB-5lel: Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_...

ID or keywords:

Entry

Database: PDB / ID: 5lel

Title

Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_10_3G124 in complex with Maltose-binding Protein and Green Fluorescent Protein

Components

DD_Off7_10_3G124
Green fluorescent protein
Maltose-binding periplasmic protein

Keywords

FLUORESCENT PROTEIN / X-ray crystallography / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions

Function / homology

Function and homology information

carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / bioluminescence / generation of precursor metabolites and energy / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

synthetic construct (others)

Escherichia coli K-12 (bacteria)

Aequorea victoria (jellyfish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Batyuk, A. / Wu, Y. / Mittl, P.R. / Plueckthun, A.

Funding support

Switzerland, 2items

Citation

Journal: Sci Rep / Year: 2017
Title: Rigidly connected multispecific artificial binders with adjustable geometries.
Authors: Wu, Y. / Batyuk, A. / Honegger, A. / Brandl, F. / Mittl, P.R.E. / Pluckthun, A.

History

Deposition	Jun 30, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2	Mar 20, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.4	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5lel.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb5lel.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	5lel.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5lel_validation.pdf.gz	517.6 KB	Display	wwPDB validaton report
Full document	5lel_full_validation.pdf.gz	547.4 KB	Display
Data in XML	5lel_validation.xml.gz	89.3 KB	Display
Data in CIF	5lel_validation.cif.gz	118.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/le/5lel ftp://data.pdbj.org/pub/pdb/validation_reports/le/5lel	HTTPS FTP

-
Related structure data

Related structure data	5le2C 5le3C 5le4C 5le6C 5le7C 5le8C 5le9C 5leaC 5lebC 5lecC 5ledC 5leeC 5lemC 5lw2C C: citing same article (ref.)
Similar structure data	5hbv-d 6wc3-d 3mv9-d 6cx9-d 4y2d-1 3vwj-d 3pqy-2 5xov-2 6mj6-d 4wid-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#174 - Jun 2014 GFP-like Proteins similarity (5) #42 - Jun 2003 Green Fluorescent Protein similarity (5) #205 - Jan 2017 Nuclear Pore Complex similarity (5) #221 - May 2018 Human Papillomavirus and Vaccines similarity (5) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (5)

Deposited unit

A: DD_Off7_10_3G124

B: Maltose-binding periplasmic protein

C: Green fluorescent protein

D: DD_Off7_10_3G124

E: Maltose-binding periplasmic protein

F: Green fluorescent protein

G: DD_Off7_10_3G124

H: Maltose-binding periplasmic protein

I: Green fluorescent protein

319 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DD_Off7_10_3G124

B: Maltose-binding periplasmic protein

C: Green fluorescent protein

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

2

D: DD_Off7_10_3G124

E: Maltose-binding periplasmic protein

F: Green fluorescent protein

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

3

G: DD_Off7_10_3G124

H: Maltose-binding periplasmic protein

I: Green fluorescent protein

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

Unit cell

Length a, b, c (Å)	235.000, 103.140, 156.840
Angle α, β, γ (deg.)	90.00, 131.35, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	DD_Off7_10_3G124 Mass: 34951.281 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-Blue
#2: Protein	Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein Mass: 43172.637 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: malE, Z5632, ECs5017 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-Blue / References: UniProt: P0AEY0
#3: Protein	Green fluorescent protein Mass: 28219.721 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-Blue / References: UniProt: P42212
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG3350 23.2% w/v, Sodium acetate 0.2 M, Bis-Tris propane 0.1 M, pH 8.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→46.63 Å / Num. obs: 51171 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC_1/2: 0.993 / Net I/σ(I): 5.81

-
Processing

Software

Name	Version	Classification
PHENIX	(DEV_2429)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.1→46.63 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 36.86

	R_factor	Num. reflection	% reflection
R_free	0.306	2557	5 %
R_work	0.258	-	-
obs	0.261	51133	99.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→46.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21046	0	0	0	21046

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	21514
X-RAY DIFFRACTION	f_angle_d	0.499	29197
X-RAY DIFFRACTION	f_dihedral_angle_d	8.684	12731
X-RAY DIFFRACTION	f_chiral_restr	0.04	3223
X-RAY DIFFRACTION	f_plane_restr	0.003	3821

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.0999-3.1596	0.3889	141	0.4033	2671	X-RAY DIFFRACTION	99
3.1596-3.224	0.3907	141	0.3948	2675	X-RAY DIFFRACTION	99
3.224-3.2941	0.4043	141	0.3753	2677	X-RAY DIFFRACTION	99
3.2941-3.3707	0.4029	139	0.3731	2649	X-RAY DIFFRACTION	100
3.3707-3.455	0.4367	142	0.3624	2703	X-RAY DIFFRACTION	100
3.455-3.5484	0.3572	142	0.3441	2696	X-RAY DIFFRACTION	100
3.5484-3.6528	0.4237	141	0.3281	2670	X-RAY DIFFRACTION	100
3.6528-3.7706	0.3387	141	0.3104	2680	X-RAY DIFFRACTION	100
3.7706-3.9053	0.364	142	0.3033	2693	X-RAY DIFFRACTION	100
3.9053-4.0616	0.3559	142	0.2845	2705	X-RAY DIFFRACTION	100
4.0616-4.2463	0.3052	141	0.2668	2689	X-RAY DIFFRACTION	100
4.2463-4.47	0.3102	143	0.2355	2713	X-RAY DIFFRACTION	100
4.47-4.7498	0.2639	142	0.2139	2710	X-RAY DIFFRACTION	100
4.7498-5.1162	0.2693	142	0.2244	2692	X-RAY DIFFRACTION	100
5.1162-5.6302	0.3298	142	0.2406	2706	X-RAY DIFFRACTION	100
5.6302-6.4431	0.297	145	0.2514	2742	X-RAY DIFFRACTION	100
6.4431-8.1107	0.2907	143	0.2134	2720	X-RAY DIFFRACTION	100
8.1107-46.6353	0.2118	147	0.1838	2785	X-RAY DIFFRACTION	100

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	0.6751	0.7798	0.2571	1.6219	-0.0461	0.2803	-0.8628	-0.7177	-0.0299	-0.5801	0.7166	-0.0182	0.1247	1.3047	0.0503	0.2241	0.3274	-0.0529	1.384	-0.4713	0.9594	72.1711	-37.6098	22.8368
2	0.8813	0.0223	-0.2924	0.7883	-0.4722	0.1914	-0.4507	-0.4151	-0.6018	0.0384	0.6087	0.2314	0.04	-0.4043	0.0756	0.478	-0.1276	-0.1151	0.8513	-0.378	0.5515	49.5233	-31.488	15.955
3	0.0887	-0.3974	0.1507	0.934	-0.7476	0.6149	0.3435	-0.2093	0.0668	0.2326	0.0774	0.4252	-0.2144	0.3653	-0	0.5255	-0.0282	0.0029	0.7251	0.0378	0.583	25.0238	-35.7313	39.2592
4	0.0359	0.1259	-0.0614	0.1595	-0.145	0.0699	-0.6977	0.2829	-0.0896	-0.1098	-0.466	-0.7307	-0.4271	0.0256	-0	1.5503	-0.2298	-0.0303	1.8712	0.0795	1.0281	99.5702	-23.9261	-30.3226
5	0.6832	0.3195	-0.9118	0.6838	-0.5997	1.175	-0.9118	0.4066	-0.0496	-0.1951	0.0478	0.3303	0.4979	-0.6271	-0.4532	0.8204	0.5567	-0.6055	-0.0422	0.584	0.7333	84.7026	-16.5902	-25.0262
6	0.2909	-0.1653	0.2257	0.5049	0.8167	1.8623	-0.4865	-0.9108	0.053	-0.2773	-0.8095	-0.2596	0.3876	-0.6057	-0.5952	0.2778	0.9585	0.0636	-1.054	-0.499	0.966	70.9267	-35.3974	-2.8086
7	0.6434	-0.0676	-1.258	1.6156	-1.1273	1.8038	0.0173	-0.3333	0.2328	-0.5157	-0.2986	0.0109	-0.1313	0.35	-0.0473	0.8258	0.0466	-0.1366	0.5339	-0.0058	0.7779	77.664	-24.7783	-13.0455
8	0.328	0.6848	-0.0893	0.9629	0.1529	0.3896	0.0225	-0.5978	0.0367	-0.4905	0.478	0.1341	-0.1696	0.7478	0.061	0.5184	0.0136	0.1269	0.6798	-0.0649	0.5792	49.1833	-41.7732	44.3126
9	0.1032	-0.29	-0.01	0.7989	0.0006	0.0424	-0.5712	0.1379	0.8431	1.6189	0.0108	0.7498	-1.2945	-0.1256	-0.0209	0.8949	0.0459	-0.0579	0.5471	-0.1763	0.7996	39.3418	-32.1278	59.0904
10	0.2039	-0.1874	-0.0313	0.0629	-0.0478	0.5427	-0.1486	0.1916	0.0897	-0.3052	0.3994	-0.604	0.6371	0.7324	-0.5173	0.0496	-0.6091	0.07	0.7044	-0.3559	0.9508	52.198	-41.7787	56.4617
11	0.4	0.0289	-0.3472	0.0528	0.0554	0.3363	0.1959	-0.1298	0.2546	-0.468	-0.021	0.1036	0.1221	1.2427	-0.0015	0.528	-0.0439	0.0417	0.9546	-0.1945	0.8339	56.7453	-40.2223	48.8965
12	1.5271	-0.7634	-1.1516	2.0395	-0.1204	0.6825	-0.2934	-1.3116	-0.2396	0.177	0.385	0.8764	0.3012	0.9298	0.3068	0.4748	-0.0045	0.0124	0.6873	-0.2056	0.3519	48.739	-49.0712	57.0001
13	0.2683	0.1697	-0.0229	0.06	0.0475	0.0514	-0.5365	-0.2552	-0.0104	-0.2085	-0.1931	0.176	-0.1222	0.4816	-0.014	0.5481	-0.021	0.0289	0.5524	-0.2162	0.401	40.5532	-44.8499	45.9761
14	0.504	-0.0516	-0.4699	0.1502	0.0675	0.6078	0.4691	0.9736	0.0297	0.3802	-0.2404	0.7612	-0.4813	0.274	0.1054	0.6278	-0.03	0.1126	0.3526	0.2378	0.7876	12.3708	-4.2225	9.174
15	0.5852	-0.0191	0.448	-0.0844	0.1011	0.713	-0.114	0.0103	0.2635	0.0874	0.1305	0.0513	0.5868	-0.0141	-0.0001	0.9086	-0.1054	0.2361	0.567	0.073	0.7273	1.4793	-24.8677	31.9573
16	0.3682	0.3648	-0.077	0.4738	0.402	0.5197	0.2099	0.1204	0.0018	0.2216	-0.4646	0.026	-0.0013	-0.1884	-0	0.6812	0.0644	0.1018	0.7781	0.0671	0.4254	-10.0758	-14.953	52.3246
17	0.1123	0.122	0.1131	0.1903	0.1206	0.1022	0.1226	-0.566	0.6428	0.1591	0.0687	0.2556	0.2946	0.0618	0.0004	1.2455	0.2297	0.2384	1.0229	0.211	0.7889	46.5264	-14.9492	-41.2708
18	0.8475	0.4928	-0.5081	0.7498	0.074	0.5144	0.2584	0.1183	-0.0845	-0.15	-0.2636	-0.4831	0.5565	0.1112	-0	1.0696	0.2407	0.0408	0.6802	0.0974	0.5207	35.1091	-24.8078	-33.0171
19	0.2787	0.1389	-0.2021	0.4624	0.0817	0.1105	0.451	-0.161	0.2446	-0.0486	-0.0185	0.3919	0.4613	0.4633	0.0002	0.6636	0.013	-0.0636	0.4833	-0.0081	0.685	29.3501	-12.7881	-3.8216
20	0.4884	-0.5835	-0.0696	1.388	-0.5506	1.4689	0.3677	0.0073	0.0728	-0.1635	0.0235	-0.033	0.1282	0.1035	-0.0001	0.598	0.0099	-0.0598	0.2939	-0.0357	0.5705	28.6144	-17.1517	-15.0744
21	0.3661	-0.5163	0.0671	0.5218	-0.3109	0.4756	0.1262	-0.0521	-0.0575	0.2744	-0.4462	-0.2485	0.7362	0.2375	-0.0003	0.8859	0.2273	0.111	0.8645	0.0451	0.6872	45.2382	-22.2715	-25.5041
22	0.4291	0.4444	-0.0773	0.482	-0.2208	0.2698	-0.259	1.0257	0.2511	-1.1236	0.0103	0.1664	0.4445	0.7022	-0.3548	1.5019	0.6064	-0.3494	1.0742	-0.2638	0.0426	16.1901	-17.2398	-20.835
23	0.0207	-0.0151	-0.0354	0.0037	0.015	0.0705	0.2826	0.1641	0.1943	0.2638	-0.4959	0.2411	-0.7179	-0.1487	0.0019	1.092	0.1836	-0.0881	1.0914	-0.319	0.5953	8.9504	-21.6533	-14.4282
24	0.2346	0.1402	0.4267	0.6846	0.6351	1.3659	0.4949	0.1568	0.1528	-0.1892	-0.0764	-0.5065	-0.0973	-1.2824	0.1273	0.7184	0.021	0.1913	0.7692	0.2911	0.7785	-5.773	0.6081	32.082
25	0.3033	-0.4422	0.2408	0.6814	-0.0333	0.5801	0.1161	0.4554	-0.0632	0.515	0.1919	-0.0301	-0.2245	-0.26	0.0001	0.5697	0.1501	0.0969	0.5341	-0.0408	0.5538	-9.0506	4.3056	38.1858
26	0.8524	-0.4332	-0.3851	1.376	1.3269	0.9972	0.6937	0.3399	0.7363	-0.2327	-0.1521	0.0881	-0.2567	-0.2183	0.0109	0.6267	0.0532	0.1322	0.7416	0.2179	0.6978	-8.9814	12.2634	37.6207
27	0.3403	0.6391	0.3856	2.0027	1.2033	0.5804	-0.0461	0.5552	0.3709	-0.0698	0.5233	-0.9563	-0.0034	-0.3677	0.5176	0.4746	0.045	-0.0567	0.6559	0.3368	0.3011	-4.2594	-0.0303	42.4402
28	0.4169	0.5305	-0.1796	0.6567	0.248	0.7223	-0.2122	0.1081	0.1634	-0.4486	-0.3288	-0.106	0.5536	0.6608	-0	0.9315	0.1662	-0.0815	0.7082	0.2253	0.6433	71.379	-12.7155	34.7957
29	0.9106	-0.4315	-1.1511	1.3892	-0.2021	1.2705	-0.4025	0.1607	0.125	0.0502	0.3368	-0.9406	0.0342	-0.3427	-0.1928	0.6994	0.1123	-0.1463	0.6308	0.1161	1.2018	86.8698	5.7353	3.02
30	0.1289	0.0501	-0.1095	0.022	0.004	0.0718	1.2373	-0.6931	0.4096	0.4895	0.2762	-0.1054	-0.2619	0.0531	0.0019	1.7347	0.6145	0.2707	2.3985	0.3637	1.6229	23.5143	-0.68	72.5004
31	2.0105	0.3389	0.7702	0.4775	0.4719	0.5472	1.0787	0.8754	-0.1178	1.8363	-0.7773	0.2738	0.0004	-0.1832	0.4035	1.7466	0.7216	0.5865	2.2771	0.9606	1.4034	19.8745	-12.6779	66.0584
32	0.088	-0.0773	0.147	0.3437	-0.0258	0.4382	-1.1722	-1.9445	-0.8456	0.6891	0.6922	0.5642	-0.0053	-0.1721	-0.0269	0.6895	0.2439	0.0848	1.0795	0.0415	1.0975	24.4729	0.3524	53.3671
33	0.7037	-0.3023	-0.8133	-0.1353	0.3925	0.8194	-0.2069	-0.8994	0.2734	0.1114	0.0967	0.0573	0.0355	0.0004	0	0.7262	0.1089	-0.1635	0.6872	0.087	0.8137	48.1508	-3.3482	42.8001
34	2.5062	0.9662	-0.2005	0.5945	0.1468	0.3628	-0.4934	-3.033	0.6524	-0.1177	-0.3908	0.3439	0.2009	0.0581	-0.4095	0.7325	0.7474	-0.5425	1.8309	0.1744	0.2329	41.4173	-0.2567	54.6593
35	0.3542	0.0796	0.0417	0.6182	-0.444	0.3096	-0.5076	0.193	0.0695	0.0249	0.7794	-0.4214	0.2823	0.2255	-0.0063	1.0306	0.4254	0.0197	1.3197	-0.4443	1.1602	30.2896	6.733	60.2922
36	0.0797	0.1014	0.0793	0.1008	0.0948	0.0906	-0.3602	-0.5936	-1.0914	-0.5887	0.049	0.4348	-0.259	-0.5872	-0.0042	0.5989	0.045	0.1566	0.8548	0.0448	0.9124	39.2795	-14.9844	35.8246
37	1.8451	0.9467	-0.8222	0.579	-0.416	0.3211	-1.3276	0.0545	0.2703	0.8768	0.9214	-0.1553	0.9444	-0.1869	-0.2872	1.3118	0.3327	-0.2462	0.7428	0.0225	0.5479	93.703	-11.7436	13.8365
38	0.2655	-0.0164	-0.1028	0.0036	0.0143	0.1486	0.0021	-0.5373	-0.1017	0.1348	0.0847	-0.0605	0.4373	0.3713	0.0062	2.3184	1.755	-1.1897	1.7913	-0.3869	1.142	99.9907	-9.0929	22.9299
39	1.2159	1.1086	-1.0913	1.1566	-1.0079	1.0482	-1.5533	-0.6999	-0.2207	0.1605	0.4904	-0.2628	1.0666	0.2089	-0.8193	1.2281	0.5578	-0.6563	1.1293	0.023	1.4437	102.8459	-15.4916	15.8348
40	0.7299	0.4592	-0.5581	0.5372	-0.4366	0.5818	-0.9466	-1.3067	-0.1987	0.5984	0.7648	-0.7417	-0.1674	-0.8983	-0.1444	1.2134	0.09	-0.5308	1.2426	-0.1977	1.8257	112.1581	-15.7436	13.8108
41	0.1441	-0.0418	-0.3181	-0.1391	-0.0963	0.5466	-0.8909	-0.3667	-0.297	-0.3966	0.7266	-0.3605	-0.3303	0.2221	-0.0106	0.9923	0.1083	-0.1817	1.0718	-0.2915	0.9662	103.4568	-11.6016	11.878

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 12 THROUGH 101 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 102 THROUGH 180 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 181 THROUGH 324 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 5 THROUGH 42 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 43 THROUGH 118 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 119 THROUGH 164 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 165 THROUGH 372 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 2 THROUGH 68 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 69 THROUGH 81 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 82 THROUGH 104 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 105 THROUGH 128 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 129 THROUGH 198 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 199 THROUGH 230 )
14	X-RAY DIFFRACTION	14	CHAIN 'D' AND (RESID 12 THROUGH 158 )
15	X-RAY DIFFRACTION	15	CHAIN 'D' AND (RESID 159 THROUGH 225 )
16	X-RAY DIFFRACTION	16	CHAIN 'D' AND (RESID 226 THROUGH 324 )
17	X-RAY DIFFRACTION	17	CHAIN 'E' AND (RESID 5 THROUGH 42 )
18	X-RAY DIFFRACTION	18	CHAIN 'E' AND (RESID 43 THROUGH 118 )
19	X-RAY DIFFRACTION	19	CHAIN 'E' AND (RESID 119 THROUGH 164 )
20	X-RAY DIFFRACTION	20	CHAIN 'E' AND (RESID 165 THROUGH 273 )
21	X-RAY DIFFRACTION	21	CHAIN 'E' AND (RESID 274 THROUGH 333 )
22	X-RAY DIFFRACTION	22	CHAIN 'E' AND (RESID 334 THROUGH 351 )
23	X-RAY DIFFRACTION	23	CHAIN 'E' AND (RESID 352 THROUGH 373 )
24	X-RAY DIFFRACTION	24	CHAIN 'F' AND (RESID 2 THROUGH 48 )
25	X-RAY DIFFRACTION	25	CHAIN 'F' AND (RESID 49 THROUGH 81 )
26	X-RAY DIFFRACTION	26	CHAIN 'F' AND (RESID 82 THROUGH 198 )
27	X-RAY DIFFRACTION	27	CHAIN 'F' AND (RESID 199 THROUGH 230 )
28	X-RAY DIFFRACTION	28	CHAIN 'G' AND (RESID 13 THROUGH 134 )
29	X-RAY DIFFRACTION	29	CHAIN 'G' AND (RESID 135 THROUGH 323 )
30	X-RAY DIFFRACTION	30	CHAIN 'H' AND (RESID 8 THROUGH 31 )
31	X-RAY DIFFRACTION	31	CHAIN 'H' AND (RESID 32 THROUGH 58 )
32	X-RAY DIFFRACTION	32	CHAIN 'H' AND (RESID 59 THROUGH 118 )
33	X-RAY DIFFRACTION	33	CHAIN 'H' AND (RESID 119 THROUGH 218 )
34	X-RAY DIFFRACTION	34	CHAIN 'H' AND (RESID 219 THROUGH 273 )
35	X-RAY DIFFRACTION	35	CHAIN 'H' AND (RESID 274 THROUGH 333 )
36	X-RAY DIFFRACTION	36	CHAIN 'H' AND (RESID 334 THROUGH 373 )
37	X-RAY DIFFRACTION	37	CHAIN 'I' AND (RESID 2 THROUGH 48 )
38	X-RAY DIFFRACTION	38	CHAIN 'I' AND (RESID 49 THROUGH 68 )
39	X-RAY DIFFRACTION	39	CHAIN 'I' AND (RESID 69 THROUGH 148 )
40	X-RAY DIFFRACTION	40	CHAIN 'I' AND (RESID 149 THROUGH 175 )
41	X-RAY DIFFRACTION	41	CHAIN 'I' AND (RESID 176 THROUGH 230 )

-
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