PDB-6nqn: Crystal structure of fast switching M159T mutant of fluorescent p...

ID or keywords:

Entry

Database: PDB / ID: 6nqn

Title

Crystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2), Y63(3-BrY)

Components

Fluorescent protein Dronpa

Keywords

FLUORESCENT PROTEIN / Dronpa2

Function / homology

Function and homology information

bioluminescence / generation of precursor metabolites and energy / metal ion binding / identical protein binding
Similarity search - Function

Biological species

Echinophyllia sp. SC22 (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Lin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	27738	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	118044	United States

Citation

Journal: Science / Year: 2020
Title: Electrostatic control of photoisomerization pathways in proteins.
Authors: Romei, M.G. / Lin, C.Y. / Mathews, I.I. / Boxer, S.G.

History

Deposition	Jan 21, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Jan 15, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4	Feb 5, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6nqn.cif.gz	732.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6nqn.ent.gz	607.5 KB	Display	PDB format
PDBx/mmJSON format	6nqn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6nqn_validation.pdf.gz	512.1 KB	Display	wwPDB validaton report
Full document	6nqn_full_validation.pdf.gz	541.4 KB	Display
Data in XML	6nqn_validation.xml.gz	78 KB	Display
Data in CIF	6nqn_validation.cif.gz	105 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nq/6nqn ftp://data.pdbj.org/pub/pdb/validation_reports/nq/6nqn	HTTPS FTP

-
Related structure data

Related structure data	6nqjC 6nqkC 6nqlC 6nqoC 6nqpC 6nqqC 6nqrC 6nqsC 6nqvC 4utsS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6nqo-2 6nqo-1 6nqr-2 6nqs-1 6nqr-1 4ppl-d 4dxn-1 1zgq-2 6nqq-2 2gx0-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
Related items in Molecule of the Month	#174 - Jun 2014 GFP-like Proteins similarity (4) #42 - Jun 2003 Green Fluorescent Protein similarity (4)

Deposited unit

A: Fluorescent protein Dronpa

B: Fluorescent protein Dronpa

C: Fluorescent protein Dronpa

D: Fluorescent protein Dronpa

E: Fluorescent protein Dronpa

F: Fluorescent protein Dronpa

G: Fluorescent protein Dronpa

H: Fluorescent protein Dronpa

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

1

A: Fluorescent protein Dronpa

B: Fluorescent protein Dronpa

C: Fluorescent protein Dronpa

E: Fluorescent protein Dronpa

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

2

D: Fluorescent protein Dronpa

F: Fluorescent protein Dronpa

G: Fluorescent protein Dronpa

H: Fluorescent protein Dronpa

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

Unit cell

Length a, b, c (Å)	71.390, 79.490, 85.650
Angle α, β, γ (deg.)	89.92, 92.40, 94.89
Int Tables number	1
Space group name H-M	P1

#1: Protein	Fluorescent protein Dronpa Mass: 29040.475 Da / Num. of mol.: 8 / Mutation: M159T, E218G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5TLG6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1106 / 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: 2.08 Å³/Da / Density % sol: 40.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl at pH 7.4, 0.1 M MgCl2, 15% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.1→37.61 Å / Num. obs: 106887 / % possible obs: 97.7 % / Redundancy: 6 % / B_iso Wilson estimate: 31 Å² / CC_1/2: 0.996 / R_rim(I) all: 0.139 / Net I/σ(I): 9.2
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7389 / CC_1/2: 0.691 / R_rim(I) all: 0.84 / % possible all: 91.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13RC2_2986: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4UTS

4uts

Resolution: 2.1→37.61 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.22

	R_factor	Num. reflection	% reflection
R_free	0.204	5345	5 %
R_work	0.172	-	-
obs	0.173	106850	97.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→37.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13975	0	0	1106	15081

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	14600
X-RAY DIFFRACTION	f_angle_d	1.192	19746
X-RAY DIFFRACTION	f_dihedral_angle_d	11.065	11890
X-RAY DIFFRACTION	f_chiral_restr	0.069	2014
X-RAY DIFFRACTION	f_plane_restr	0.008	2582

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 (%)
2.1-2.1238	0.2825	164	0.2352	3115	X-RAY DIFFRACTION	91
2.1238-2.1488	0.2795	170	0.2297	3228	X-RAY DIFFRACTION	92
2.1488-2.175	0.2868	164	0.2228	3100	X-RAY DIFFRACTION	91
2.175-2.2025	0.27	168	0.221	3201	X-RAY DIFFRACTION	93
2.2025-2.2315	0.2521	183	0.2123	3473	X-RAY DIFFRACTION	99
2.2315-2.2621	0.26	180	0.206	3416	X-RAY DIFFRACTION	99
2.2621-2.2944	0.2717	180	0.2185	3429	X-RAY DIFFRACTION	99
2.2944-2.3286	0.2881	181	0.2186	3433	X-RAY DIFFRACTION	99
2.3286-2.365	0.2233	178	0.2076	3383	X-RAY DIFFRACTION	98
2.365-2.4038	0.2453	180	0.2074	3425	X-RAY DIFFRACTION	99
2.4038-2.4452	0.2539	178	0.2117	3382	X-RAY DIFFRACTION	98
2.4452-2.4897	0.2938	175	0.215	3319	X-RAY DIFFRACTION	95
2.4897-2.5375	0.2467	177	0.1956	3373	X-RAY DIFFRACTION	98
2.5375-2.5893	0.2304	182	0.1902	3459	X-RAY DIFFRACTION	100
2.5893-2.6456	0.2287	184	0.1819	3493	X-RAY DIFFRACTION	100
2.6456-2.7071	0.2283	178	0.1868	3380	X-RAY DIFFRACTION	99
2.7071-2.7748	0.2119	183	0.1854	3472	X-RAY DIFFRACTION	99
2.7748-2.8498	0.2458	182	0.1967	3464	X-RAY DIFFRACTION	99
2.8498-2.9336	0.277	179	0.1982	3408	X-RAY DIFFRACTION	99
2.9336-3.0283	0.2456	180	0.1984	3410	X-RAY DIFFRACTION	99
3.0283-3.1365	0.2256	179	0.1888	3405	X-RAY DIFFRACTION	98
3.1365-3.262	0.2067	175	0.1797	3318	X-RAY DIFFRACTION	96
3.262-3.4104	0.1985	182	0.1628	3460	X-RAY DIFFRACTION	100
3.4104-3.59	0.2033	181	0.1644	3443	X-RAY DIFFRACTION	100
3.59-3.8147	0.1734	180	0.1526	3424	X-RAY DIFFRACTION	100
3.8147-4.109	0.1678	183	0.1389	3466	X-RAY DIFFRACTION	99
4.109-4.5218	0.1233	180	0.1208	3428	X-RAY DIFFRACTION	99
4.5218-5.1747	0.1427	177	0.1188	3352	X-RAY DIFFRACTION	97
5.1747-6.5141	0.1513	183	0.1459	3482	X-RAY DIFFRACTION	100
6.5141-37.6156	0.19	179	0.1719	3364	X-RAY DIFFRACTION	98

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	3.0575	-0.7181	-0.3436	5.0228	1.9432	2.2866	-0.0945	-0.2033	0.4719	0.2433	0.4783	-0.5763	-0.0295	0.649	-0.3924	0.1929	-0.0282	-0.0023	0.3163	-0.0728	0.3698	-8.221	23.1435	-2.2753
2	1.0929	-0.2688	-0.3251	1.5073	-0.0124	2.3953	0.006	-0.1644	0.1745	0.0899	0.1289	-0.219	-0.0265	0.2422	-0.1373	0.1775	-0.0109	0.0014	0.2684	-0.0924	0.2656	-15.2114	17.381	0.0506
3	2.1761	0.2974	-1.6953	3.9973	-0.7793	7.5472	0.112	0.1739	0.1794	-0.217	0.1471	-0.0185	-0.3081	0.1653	-0.24	0.0399	-0.0286	-0.0495	0.1895	-0.0453	0.1935	-23.648	16.6406	-9.7952
4	4.0971	-3.5687	4.193	6.1696	-5.7411	8.8011	-0.0147	0.1148	0.0266	-0.075	0.2022	-0.0448	-0.0195	-0.0449	-0.3388	0.1604	-0.0502	0.0241	0.2518	-0.0517	0.2382	-25.4286	15.9913	-5.8743
5	2.5901	0.5875	-1.6864	2.8878	-1.0362	4.7917	0.0657	-0.02	0.4338	0.2078	0.0794	-0.1296	-0.3409	0.0337	-0.1251	0.1655	-0.0069	-0.0328	0.2007	-0.0881	0.2759	-19.0285	24.2087	-0.4713
6	0.8443	-0.212	0.4104	0.0479	-0.1021	0.2162	0.3255	-0.2133	0.741	1.7387	-1.0585	1.7894	0.3242	-0.2353	0.6921	0.6217	-0.1279	0.2674	0.4847	-0.2527	0.8144	-39.0043	31.6279	12.627
7	3.0802	-0.3867	-0.4794	6.0552	2.1509	1.9305	0.0031	-0.0876	0.2795	0.1549	-0.0967	0.9427	-0.0956	-0.2105	0.1318	0.228	0.0092	0.0416	0.372	-0.011	0.29	-58.0586	15.3678	-1.3307
8	0.8993	0.4177	-0.2343	1.5375	-0.2924	1.5662	0.053	-0.1162	0.1667	0.063	-0.0134	0.2576	0.033	-0.1182	-0.0446	0.2075	0.0112	0.0359	0.2451	0.0036	0.23	-48.5283	15.0741	-2.8481
9	4.447	-3.6131	5.3402	6.4643	-6.5888	9.5372	0.0926	-0.142	0.0015	0.0216	-0.0085	-0.0051	-0.0913	0.0769	0.0066	0.202	0.0007	0.0331	0.211	-0.0193	0.2084	-39.0759	12.6296	-2.4312
10	2.8926	1.2519	-1.6165	3.488	-1.1407	4.3578	0.1717	-0.2136	0.2556	0.2209	-0.1743	0.0469	-0.3101	-0.0338	-0.0368	0.1743	0.0605	0.0358	0.1935	-0.0219	0.2342	-45.2586	21.514	0.763
11	4.0226	-1.3564	-1.756	6.6457	4.9253	5.8478	0.1552	0.3668	-0.1466	-0.765	0.422	-0.645	-0.3671	0.6429	-0.5745	0.312	0.0601	-0.0135	0.357	-0.0617	0.3456	-4.3578	-8.3566	-17.2392
12	1.2607	0.0604	-0.0208	1.3273	0.1139	1.8646	0.0098	0.0581	-0.1966	0.058	0.1699	-0.2292	0.11	0.1799	-0.1755	0.2159	0.0431	-0.0252	0.2551	-0.0878	0.2586	-14.8902	-8.1177	-14.9728
13	0.5332	-0.876	-1.0085	1.3802	1.6496	1.9273	0.8392	0.1199	-1.1931	-1.0002	-1.0762	0.8571	-0.1125	0.2586	0.3232	0.6753	0.0432	-0.1526	0.5823	-0.2386	0.7187	-31.7152	-24.8082	-31.028
14	3.7719	1.3428	-2.7644	6.539	-5.1275	7.4191	0.0203	-0.1682	-0.2608	0.6036	0.4174	0.5542	-0.3249	-0.6941	-0.443	0.2575	-0.0457	-0.0414	0.2718	0.0565	0.3233	-60.6836	26.9602	-44.855
15	1.0047	0.0349	0.1235	1.7601	-0.1848	2.6682	0.0381	-0.0976	-0.2074	-0.0423	0.147	0.2869	0.0327	-0.2531	-0.2073	0.1694	0.0035	-0.0154	0.2641	0.0782	0.2797	-54.6447	28.9595	-45.3213
16	1.9524	0.2487	1.709	4.797	0.684	5.9224	0.041	0.1196	-0.1938	-0.3246	0.0879	0.0053	0.2672	-0.0282	-0.1139	0.0491	-0.0225	0.0441	0.1764	0.0194	0.1993	-43.9983	31.467	-53.4572
17	5.822	-5.5507	-5.1983	7.6425	6.208	5.3793	-0.0512	-0.1923	-0.1247	-0.2957	0.2029	0.0822	-0.2585	0.3111	-0.3379	0.1811	-0.0408	-0.0243	0.2144	0.0354	0.2212	-42.5541	32.0648	-49.2915
18	2.3438	0.6415	0.9211	3.1936	1.1617	3.6954	-0.053	0.0423	-0.3745	0.0433	0.1684	0.1703	0.1618	0.0179	-0.1095	0.2062	-0.0074	0.0139	0.2399	0.0885	0.3	-49.3052	23.8312	-44.5792
19	0.5091	-1.6999	1.6847	5.6046	-5.4646	5.3003	0.7886	-0.9752	-1.519	1.8953	-0.8512	-1.1178	-0.5382	-0.3163	0.1167	0.7166	-0.1121	-0.296	0.5941	0.2863	0.9476	-30.9616	16.2275	-29.9536
20	2.9733	-1.798	0.5037	9.0832	0.7181	2.0876	0.0533	0.2156	-0.4296	-0.0027	-0.0347	0.7678	0.2537	-0.2848	-0.0139	0.2339	-0.0596	-0.0066	0.3575	-0.0165	0.2606	-54.1722	-11.7616	-21.4496
21	1.0708	-0.0673	0.0921	2.2391	-0.3865	2.0057	0.006	0.1489	-0.2003	0.092	0.0992	0.0567	0.1823	-0.0792	-0.1086	0.2514	-0.0419	-0.0163	0.2403	0.0016	0.2275	-44.792	-11.4594	-15.9473
22	4.4213	5.1526	-0.4078	9.6231	-0.2229	3.7723	0.1658	0.1245	-0.3126	0.3456	-0.0939	0.099	0.0414	-0.144	-0.0639	0.1871	-0.0001	-0.0161	0.2291	0.0147	0.2679	-52.9594	-9.2772	-13.6228
23	8.3946	1.6984	5.1581	8.8926	7.9853	8.8978	0.1554	0.6498	0.4325	-0.6198	-0.0141	-0.1042	-0.6345	-0.0402	-0.0266	0.2986	0.0386	-0.0086	0.2748	0.0956	0.2033	-42.5586	9.3121	-25.3711
24	1.4651	-0.9219	1.5234	7.1979	-6.6657	7.281	0.0895	0.0992	-0.1282	0.1722	-0.0295	0.155	-0.2159	0.428	0.016	0.2059	-0.0172	-0.0045	0.2776	-0.0223	0.1906	-36.0587	-8.7083	-16.3373
25	6.7479	5.6939	-5.427	6.1472	-4.7984	4.365	0.0049	-0.0047	-0.0921	-0.1025	-0.1623	-0.187	0.1561	0.1828	0.1319	0.2132	0.0277	-0.0232	0.156	-0.0157	0.2052	-37.7329	-3.9173	-17.8355
26	3.219	-1.1092	1.3798	2.0807	0.0124	2.2899	0.1343	0.4604	-0.3036	-0.1062	-0.1375	0.1654	0.1577	0.0902	-0.0221	0.2133	-0.0613	-0.0165	0.2346	-0.0541	0.2188	-43.4152	-13.8659	-21.4187
27	1.9637	-1.6625	-1.1157	5.7555	0.9935	8.539	-0.3431	-0.3502	-1.2274	-0.2054	0.1145	-0.8053	1.4724	0.7061	0.1208	0.5246	0.1206	-0.0545	0.0624	-0.0719	0.7882	-24.4149	-22.5289	-16.3625
28	2.6414	-1.2051	0.9471	9.4375	-2.8377	2.438	-0.0555	-0.1209	-0.062	0.0835	-0.026	-0.9114	-0.0121	0.3636	0.0891	0.1973	-0.0214	0.0112	0.4359	-0.0466	0.2686	-10.3267	33.031	-42.1628
29	0.9234	-0.1424	0.114	2.7335	0.313	1.6126	0.0387	-0.1436	-0.1329	0.0253	0.0088	-0.269	-0.0122	0.1644	-0.0633	0.2422	0.0026	-0.0168	0.3087	-0.024	0.2563	-17.2523	31.31	-45.2616
30	5.6138	-1.5291	4.127	3.4012	-3.2138	4.5239	-0.1183	-0.5444	0.104	0.7266	0.2678	-0.2171	-0.5188	0.1988	-0.2053	0.3939	0.0003	-0.0181	0.2487	-0.0725	0.1975	-26.0982	50.5852	-36.5819
31	2.1509	-0.4012	0.1008	6.785	5.8843	5.9664	0.1521	-0.1301	-0.1378	-0.4438	-0.1264	-0.1888	-0.5267	-0.4383	0.0547	0.1963	-0.0131	0.0101	0.2451	0.013	0.1758	-29.4865	31.71	-45.5158
32	7.6681	-5.5926	-5.7373	7.3189	5.241	4.6673	0.0953	0.189	-0.2617	0.1984	-0.3709	0.1044	-0.0101	-0.4149	0.2136	0.2406	0.0181	-0.027	0.1793	-0.0162	0.1971	-28.8276	36.6375	-44.4243
33	2.4271	1.323	1.6962	3.6514	1.8843	4.8607	0.1318	-0.303	-0.0657	0.2901	-0.1695	0.0377	0.3215	-0.059	0.0465	0.1617	0.056	-0.0067	0.2477	0.0309	0.2295	-23.3551	26.5617	-41.0655
34	3.7769	-1.5068	2.9259	5.0191	-4.5062	8.4941	0.0845	0.2978	0.1095	-0.6993	0.4157	0.6331	0.0124	-0.7675	-0.4407	0.4232	0.1019	-0.0082	0.3696	0.0969	0.3319	-55.6133	-22.9124	-61.9894
35	1.2058	-0.239	-0.1394	1.5154	-0.151	2.7071	0.0044	0.0347	0.085	0.0334	0.1672	0.2983	-0.2373	-0.3306	-0.1945	0.2814	0.0401	0.0184	0.2329	0.068	0.2663	-47.2637	-24.03	-59.0631
36	3.0429	3.0685	3.1567	7.658	5.6165	4.5434	0.0306	-0.0368	-0.0434	0.2009	0.1811	0.157	0.2575	0.206	-0.1947	0.2289	0.0428	0.0085	0.2712	0.0573	0.2337	-37.3634	-24.8988	-56.0293
37	4.44	-0.0214	-1.4418	1.0991	-1.5086	3.0934	0.1562	0.1713	0.2593	-0.3315	0.1906	0.0115	-0.2439	0.1477	-0.3465	0.3597	0.0226	-0.019	0.195	0.1042	0.2356	-41.684	-20.352	-66.2592
38	4.466	-0.0262	-6.2007	2.1319	-0.1473	9.0948	0.2284	0.0029	0.7681	0.3556	0.2272	0.1799	-0.66	-0.4072	-0.6758	0.4146	0.122	0.0205	0.3375	0.0558	0.3533	-49.5025	-14.6441	-54.5202
39	0.171	0.1079	0.3372	0.0641	0.2245	0.7482	0.5263	0.1258	1.344	-0.378	-0.9318	-0.2335	0.1833	-0.3773	0.1695	0.5894	0.0959	0.0428	0.5013	0.2389	0.7219	-27.7534	-6.5404	-73.8142
40	2.742	-1.1866	0.1138	8.0165	-2.3109	2.7988	-0.0525	0.0672	0.5097	0.276	0.025	-0.9815	-0.3552	0.1709	0.0944	0.3181	-0.1094	0.0509	0.3551	-0.0131	0.3053	-5.056	-20.1816	-60.6568
41	1.2595	-0.5523	-0.2673	2.4516	0.3964	1.5267	0.0618	0.0885	0.2843	-0.0169	-0.0131	-0.2757	-0.2426	0.217	-0.0538	0.3639	-0.0896	0.0568	0.2837	-0.0078	0.2662	-12.32	-19.8815	-58.1231
42	7.0903	0.4101	-2.4956	7.4048	-5.2147	7.4957	0.0254	0.4053	0.0046	-1.0641	0.1043	-0.2805	0.3267	-0.088	-0.1111	0.3615	0.035	0.0566	0.225	-0.0728	0.199	-17.2693	-40.2941	-67.8054
43	3.6721	-1.8768	-2.3754	5.4466	5.4313	6.2428	-0.0904	0.209	0.1955	0.405	-0.0802	-0.1507	0.4587	-0.3973	0.1953	0.3427	-0.0425	0.0238	0.2183	0.0389	0.1894	-24.2943	-22.3346	-58.7785
44	4.7617	3.4615	4.3313	6.3301	4.6216	6.0195	-0.0122	0.0106	0.0729	-0.3232	-0.2486	0.0435	-0.1798	-0.3959	0.1965	0.312	-0.0076	0.0718	0.1951	0.0086	0.2231	-22.6126	-27.2867	-60.2558
45	3.394	-0.8809	-1.3977	2.5593	0.6287	3.2468	0.1379	0.2932	0.2114	-0.2727	-0.1512	-0.1374	-0.4715	0.0267	-0.0143	0.3731	-0.0731	0.0261	0.21	0.0358	0.2182	-18.7826	-16.1912	-62.7637

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 46 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 47 THROUGH 123 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 124 THROUGH 151 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 152 THROUGH 179 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 180 THROUGH 216 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 217 THROUGH 228 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 3 THROUGH 32 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 33 THROUGH 151 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 152 THROUGH 179 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 180 THROUGH 221 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 4 THROUGH 20 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 21 THROUGH 216 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 217 THROUGH 227 )
14	X-RAY DIFFRACTION	14	CHAIN 'D' AND (RESID 3 THROUGH 20 )
15	X-RAY DIFFRACTION	15	CHAIN 'D' AND (RESID 21 THROUGH 123 )
16	X-RAY DIFFRACTION	16	CHAIN 'D' AND (RESID 124 THROUGH 151 )
17	X-RAY DIFFRACTION	17	CHAIN 'D' AND (RESID 152 THROUGH 179 )
18	X-RAY DIFFRACTION	18	CHAIN 'D' AND (RESID 180 THROUGH 216 )
19	X-RAY DIFFRACTION	19	CHAIN 'D' AND (RESID 217 THROUGH 228 )
20	X-RAY DIFFRACTION	20	CHAIN 'E' AND (RESID 3 THROUGH 46 )
21	X-RAY DIFFRACTION	21	CHAIN 'E' AND (RESID 47 THROUGH 99 )
22	X-RAY DIFFRACTION	22	CHAIN 'E' AND (RESID 100 THROUGH 123 )
23	X-RAY DIFFRACTION	23	CHAIN 'E' AND (RESID 124 THROUGH 135 )
24	X-RAY DIFFRACTION	24	CHAIN 'E' AND (RESID 136 THROUGH 163 )
25	X-RAY DIFFRACTION	25	CHAIN 'E' AND (RESID 164 THROUGH 179 )
26	X-RAY DIFFRACTION	26	CHAIN 'E' AND (RESID 180 THROUGH 216 )
27	X-RAY DIFFRACTION	27	CHAIN 'E' AND (RESID 217 THROUGH 220 )
28	X-RAY DIFFRACTION	28	CHAIN 'F' AND (RESID 3 THROUGH 32 )
29	X-RAY DIFFRACTION	29	CHAIN 'F' AND (RESID 33 THROUGH 123 )
30	X-RAY DIFFRACTION	30	CHAIN 'F' AND (RESID 124 THROUGH 135 )
31	X-RAY DIFFRACTION	31	CHAIN 'F' AND (RESID 136 THROUGH 163 )
32	X-RAY DIFFRACTION	32	CHAIN 'F' AND (RESID 164 THROUGH 179 )
33	X-RAY DIFFRACTION	33	CHAIN 'F' AND (RESID 180 THROUGH 221 )
34	X-RAY DIFFRACTION	34	CHAIN 'G' AND (RESID 4 THROUGH 20 )
35	X-RAY DIFFRACTION	35	CHAIN 'G' AND (RESID 21 THROUGH 151 )
36	X-RAY DIFFRACTION	36	CHAIN 'G' AND (RESID 152 THROUGH 179 )
37	X-RAY DIFFRACTION	37	CHAIN 'G' AND (RESID 180 THROUGH 200 )
38	X-RAY DIFFRACTION	38	CHAIN 'G' AND (RESID 201 THROUGH 216 )
39	X-RAY DIFFRACTION	39	CHAIN 'G' AND (RESID 217 THROUGH 227 )
40	X-RAY DIFFRACTION	40	CHAIN 'H' AND (RESID 3 THROUGH 32 )
41	X-RAY DIFFRACTION	41	CHAIN 'H' AND (RESID 33 THROUGH 123 )
42	X-RAY DIFFRACTION	42	CHAIN 'H' AND (RESID 124 THROUGH 135 )
43	X-RAY DIFFRACTION	43	CHAIN 'H' AND (RESID 136 THROUGH 163 )
44	X-RAY DIFFRACTION	44	CHAIN 'H' AND (RESID 164 THROUGH 179 )
45	X-RAY DIFFRACTION	45	CHAIN 'H' AND (RESID 180 THROUGH 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