PDB-6etb: Aerobic S262Y mutation of E. coli FLRD core

ID or keywords:

Entry

Database: PDB / ID: 6etb

Title

Aerobic S262Y mutation of E. coli FLRD core

Components

Anaerobic nitric oxide reductase flavorubredoxin

Keywords

OXIDOREDUCTASE / Flavorubredoxin / flavodiiron protein / diiron center / nitric oxide reductase

Function / homology

Function and homology information

nitric oxide reductase activity / nitric oxide catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / response to nitric oxide / FMN binding / electron transfer activity / iron ion binding / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.905 Å

Authors

Borges, P.T. / Romao, C.V. / Carrondo, M.A. / Teixeira, M. / Frazao, C.

Citation

Journal: To Be Published
Title: A tyrosine mutation in E. coli flavodiiron protein increases radiation sensitivity in the crystal structure
Authors: Borges, P.T. / Romao, C.V. / Carrondo, M.A. / Teixeira, M. / Frazao, C.

History

Deposition	Oct 26, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6etb.cif.gz	352.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6etb.ent.gz	286 KB	Display	PDB format
PDBx/mmJSON format	6etb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6etb_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6etb_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6etb_validation.xml.gz	18.4 KB	Display
Data in CIF	6etb_validation.cif.gz	30.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/et/6etb ftp://data.pdbj.org/pub/pdb/validation_reports/et/6etb	HTTPS FTP

-
Related structure data

Related structure data	4d02S S: Starting model for refinement
Similar structure data	5lmc-1 5lld-1 2ohi-6 6frm-2 2ohj-d 2ohi-5 2hig-1 6frm-1 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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #133 - Jan 2011 Nitric Oxide Synthase similarity (3) #111 - Mar 2009 Hydrogenase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #41 - May 2003 Hemoglobin similarity (1) #142 - Oct 2011 PDB Pioneers similarity (4) #228 - Dec 2018 Directed Evolution of Enzymes similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2) #159 - Mar 2013 Erythrocruorin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#187 - Jul 2015
New Delhi Metallo-β-Lactamase
similarity (3)
#133 - Jan 2011
Nitric Oxide Synthase
similarity (3)
#111 - Mar 2009
Hydrogenase
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#263 - Nov 2021
Acetohydroxyacid Synthase
similarity (1)
#41 - May 2003
Hemoglobin
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (4)
#228 - Dec 2018
Directed Evolution of Enzymes
similarity (3)
#105 - Sep 2008
Ribonuclease A
similarity (2)
#159 - Mar 2013
Erythrocruorin
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#206 - Feb 2017
Globin Evolution
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)

Deposited unit

A: Anaerobic nitric oxide reductase flavorubredoxin

B: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

95.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Anaerobic nitric oxide reductase flavorubredoxin

B: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin

B: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

defined by author
Evidence: gel filtration
191 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.383, 64.407, 147.254
Angle α, β, γ (deg.)	90.00, 91.09, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	A-630- HOH

-
Protein , 1 types, 2 molecules AB

#1: Protein	Anaerobic nitric oxide reductase flavorubredoxin / FlavoRb Mass: 47104.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46877

-
Non-polymers , 5 types, 792 molecules

#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical	ChemComp-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂
#5: Chemical	ChemComp-O / OXYGEN ATOM Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.28 Å³/Da / Density % sol: 45.9 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.0 UL OF PROTEIN AT 15 MG/ML WITH 2.0 UL OF CRYSTALLIZATION SOLUTION (0.1 M SODIUM CITRATE PH 5.6, 20% (W/V) PEG 4000 AND 20% (V/V) 2-PROPANOL)

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→75.83 Å / Num. obs: 57099 / % possible obs: 80.69 % / Redundancy: 2.3 % / R_merge(I) obs: 0.113 / R_pim(I) all: 0.075 / R_rim(I) all: 0.137 / Net I/σ(I): 5.2
Reflection shell	Highest resolution: 1.9 Å / R_pim(I) all: 0.431 / R_rim(I) all: 0.863 / % possible all: 88.7

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1436	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4D02

4d02

Resolution: 1.905→75.758 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 16.64 / Phase error: 19.98
Details: The refinement of S262Y mutation from E. coli FLRD core converged to Rwork and Rfree of 0.2174 and 0.2348, respectively, using a Rfree test set size of 1.51% (799 reflections). The final ...

	R_factor	Num. reflection	% reflection
R_free	0.1998	799	1.51 %
R_work	0.1998	-	-
obs	0.1998	52943	80.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.905→75.758 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6440	0	72	782	7294

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	6725
X-RAY DIFFRACTION	f_angle_d	0.56	9123
X-RAY DIFFRACTION	f_dihedral_angle_d	10.146	2433
X-RAY DIFFRACTION	f_chiral_restr	0.022	990
X-RAY DIFFRACTION	f_plane_restr	0.002	1182

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9052-1.9269	0.3038	951	0.3038	951	X-RAY DIFFRACTION	44
1.9269-1.9496	0.2971	1310	0.2971	1310	X-RAY DIFFRACTION	60
1.9496-1.9733	0.2959	1433	0.2959	1433	X-RAY DIFFRACTION	65
1.9733-1.9983	0.2956	1465	0.2956	1465	X-RAY DIFFRACTION	68
1.9983-2.0246	0.2909	1546	0.2909	1546	X-RAY DIFFRACTION	71
2.0246-2.0524	0.2758	1549	0.2758	1549	X-RAY DIFFRACTION	73
2.0524-2.0817	0.2655	1670	0.2655	1670	X-RAY DIFFRACTION	75
2.0817-2.1128	0.2582	1664	0.2582	1664	X-RAY DIFFRACTION	77
2.1128-2.1458	0.2369	1720	0.2369	1720	X-RAY DIFFRACTION	79
2.1458-2.181	0.2396	1682	0.2396	1682	X-RAY DIFFRACTION	78
2.181-2.2186	0.2396	1708	0.2396	1708	X-RAY DIFFRACTION	78
2.2186-2.2589	0.2349	1656	0.2349	1656	X-RAY DIFFRACTION	77
2.2589-2.3024	0.2315	1927	0.2315	1927	X-RAY DIFFRACTION	87
2.3024-2.3494	0.2278	1903	0.2278	1903	X-RAY DIFFRACTION	88
2.3494-2.4005	0.2276	1950	0.2276	1950	X-RAY DIFFRACTION	90
2.4005-2.4563	0.229	1956	0.229	1956	X-RAY DIFFRACTION	90
2.4563-2.5177	0.2167	1926	0.2167	1926	X-RAY DIFFRACTION	89
2.5177-2.5858	0.2166	1958	0.2166	1958	X-RAY DIFFRACTION	89
2.5858-2.6619	0.2161	1883	0.2161	1883	X-RAY DIFFRACTION	87
2.6619-2.7478	0.2082	1782	0.2082	1782	X-RAY DIFFRACTION	81
2.7478-2.846	0.2085	1985	0.2085	1985	X-RAY DIFFRACTION	91
2.846-2.96	0.2063	1983	0.2063	1983	X-RAY DIFFRACTION	91
2.96-3.0947	0.2021	1998	0.2021	1998	X-RAY DIFFRACTION	90
3.0947-3.2579	0.1853	1950	0.1853	1950	X-RAY DIFFRACTION	89
3.2579-3.462	0.1715	1879	0.1715	1879	X-RAY DIFFRACTION	86
3.462-3.7293	0.1688	1858	0.1688	1858	X-RAY DIFFRACTION	84
3.7293-4.1045	0.1569	1947	0.1569	1947	X-RAY DIFFRACTION	89
4.1045-4.6984	0.1446	1935	0.1446	1935	X-RAY DIFFRACTION	87
4.6984-5.9191	0.1597	1849	0.1597	1849	X-RAY DIFFRACTION	83
5.9191-75.8179	0.1616	1920	0.1616	1920	X-RAY DIFFRACTION	84

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	-0.0006	-0.0179	-0.0006	0.3699	-0.1127	0.0375	0.0715	0.0254	0.0424	-0.1104	-0.002	-0.0807	0.0598	0.0569	-0	0.196	0.0216	-0.0504	0.147	-0.0076	0.1986	-28.7562	-36.6483	-9.7889
2	0.0099	0.014	-0.0447	0.0279	-0.0984	0.2909	0.4089	-0.0512	-0.1001	-0.582	0.3654	0.1737	-0.0021	-0.0409	0.0141	0.3213	0.015	0.0008	0.1587	-0.0222	0.4093	-10.9933	-25.8163	-4.6271
3	0.0437	0.1278	0.0608	0.2589	0.054	0.2222	0.0785	-0.0024	-0.1921	-0.1629	-0.0119	0.0021	0.1454	-0.0268	-0.0029	0.1536	0.0132	-0.0294	0.1311	-0.0189	0.2077	-29.9656	-31.1157	-14.0031
4	0.2566	0.0132	-0.2828	0.0554	0.1616	1.1617	0.1248	-0.042	-0.2325	-0.4486	0.187	-0.144	0.553	0.4624	0.0124	0.3956	0.0397	-0.0709	0.1957	-0.0432	0.3042	-25.23	-37.6893	-21.763
5	0.2287	-0.0421	-0.2426	0.2096	-0.0001	0.2001	0.2267	0.0432	-0.2044	0.0488	0.0223	-0.1599	0.2759	0.1489	0.0001	0.1746	0.0271	0.0182	0.1696	0.0072	0.2626	-26.655	-26.4811	-20.9155
6	0.1236	0.2225	-0.3385	0.2796	-0.0905	0.7436	-0.1397	0.1402	0.0582	-0.0487	0.0106	-0.0289	0.0506	0.1457	-0.0174	0.2209	0.0394	-0.0155	0.2003	0.0242	0.1539	-27.5933	-19.2237	-25.0901
7	0.5307	0.4441	-0.1625	0.423	0.0868	0.264	0.0768	-0.0099	-0.0881	0.0375	-0.0256	0.0167	-0.0017	0.0441	0.0793	0.0906	-0.0007	-0	0.0885	0.0336	0.1237	-32.2493	-25.226	-7.1384
8	0.0599	-0.0181	-0.0577	0.0422	-0.0066	0.042	0.0726	-0.0572	-0.078	0.027	-0.0643	0.053	0.0439	0.1788	-0.0003	0.0837	-0.0009	0.019	0.2214	0.0291	0.1444	-21.8571	-26.4606	4.6456
9	0.4174	-0.3271	0.1706	0.2058	-0.0135	0.5485	0.0141	-0.0154	-0.0251	0.2692	-0.0453	-0.018	-0.0375	-0.1281	-0.0022	0.1554	0.0249	0.0059	0.1609	0.0173	0.1502	-32.2496	-19.4622	-1.3216
10	0.0502	-0.0404	0.0816	0.1103	0.0153	0.0663	0.0798	-0.1699	0.1444	-0.1612	-0.1977	-0.0363	-0.2428	-0.4312	-0.0039	0.1218	0.0688	0.037	0.2336	0.0292	0.2304	-26.4152	-15.8917	8.7624
11	0.3343	-0.0063	0.3008	0.4662	-0.0647	0.3289	0.048	-0.3584	-0.4242	-0.0123	0.0085	-0.007	0.1177	-0.0126	0.0176	0.1301	-0.0044	-0.0039	0.2317	0.0551	0.1607	-4.5946	-19.6197	19.5008
12	0.142	-0.2019	-0.0113	0.3304	0.1246	0.4782	0.0076	-0.2626	-0.0679	-0.1257	0.044	-0.0439	-0.0595	0.0125	0.2168	0.0751	0.0092	0.0583	0.1554	0.007	0.1356	-4.1939	-17.4521	8.4502
13	0.1266	-0.1025	-0.0717	0.0598	0.0069	0.1166	0.0507	0.0344	0.107	-0.0029	0.1074	-0.0563	-0.0704	-0.2033	0.052	0.1772	0.0186	0.001	0.1391	0.0433	0.15	-12.7959	-9.7896	6.0018
14	0.0842	0.0193	0.1006	0.1794	0.1294	0.156	-0.1452	-0.1594	0.1642	-0.0233	-0.0429	-0.076	-0.113	-0.0579	-0.0476	0.1681	0.0054	-0.017	0.1088	0.0087	0.163	1.7491	-7.8407	13.5113
15	0.1706	0.1459	-0.0264	0.134	-0.0035	0.0497	-0.1585	-0.5939	0.2829	0.0657	0.1383	-0.1375	-0.3938	-0.0124	-0.0381	0.1773	-0.0001	0.0196	0.3636	-0.0502	0.1059	-2.8076	-12.5598	27.0024
16	0.0208	-0.1004	0.0515	0.2776	-0.0422	0.0238	-0.0969	-0.0486	0.0022	0.0212	-0.0287	-0.0424	-0.4201	0.0454	-0	0.2385	0.0018	-0.0135	0.1282	0.0223	0.1986	-5.5028	-30.7994	29.944
17	0.0483	0.0079	-0.0015	-0.0007	0.018	0.0367	-0.4511	-0.0246	-0.5405	0.1976	0.0278	-0.5643	-0.1435	-0.5552	0.002	0.3253	0.0649	0.0701	0.2162	-0.0457	0.3054	-1.2712	-41.5864	11.8661
18	0.1397	-0.1819	0.1672	0.4688	-0.0683	0.1089	0.0242	-0.0533	0.0949	0.0237	0.0396	-0.0514	-0.231	-0.2235	0.0001	0.2284	-0.0159	0.0356	0.1759	0.0093	0.1436	-2.3451	-36.3566	33.0067
19	1.9828	0.3951	0.5086	0.385	0.538	0.7858	-0.0551	0.5004	0.4806	0.199	0.2845	-0.3585	-0.7013	0.3176	0.0274	0.4819	-0.116	-0.1694	0.1073	0.0417	0.395	6.7258	-29.74	32.6766
20	0.2726	-0.1226	-0.1851	0.3764	-0.048	0.1135	-0.2726	0.1066	0.2622	-0.1275	-0.0447	0.1319	-0.5257	-0.0135	-0.0131	0.2984	-0.0505	-0.0398	0.1974	0.0223	0.1596	5.2372	-41.0165	33.4488
21	0.8853	-0.4714	0.36	0.5672	0.4472	0.7706	-0.1118	-0.0063	-0.0995	0.0411	0.2244	-0.095	0.068	0.1797	0.2073	0.2191	0.0224	-0.0222	0.1552	0.047	0.1508	8.4226	-48.2773	36.2748
22	0.5137	-0.1101	-0.2371	0.2771	0.3894	0.3738	0.0653	0.0419	-0.0245	0.0761	0.0242	0.0442	-0.0398	-0.1832	0.1039	0.1674	0.029	0.0179	0.1754	0.0476	0.1323	-9.5746	-42.1353	31.5778
23	0.0444	0.0086	-0.0393	0.0382	-0.0076	0.0194	0.057	0.0444	-0.1224	-0.1088	-0.1847	-0.0391	-0.361	-0.0059	-0	0.2539	0.0144	-0.0217	0.2119	0.0068	0.1315	-14.7455	-40.887	16.8183
24	0.1806	-0.1709	-0.2469	0.8224	0.4067	1.7416	0.0764	0.0879	-0.0764	-0.242	-0.4233	0.2483	-0.1118	-1.0718	-0.7156	0.0716	-0.0846	0.0203	-0.0154	0.2074	-0.0698	-14.716	-47.8434	28.8274
25	0.0738	-0.111	0.0773	0.1089	-0.0894	0.1343	0.1102	-0.1597	-0.0342	0.0933	-0.2502	-0.3379	0.1942	-0.4221	-0.0186	0.2211	-0.0464	0.0212	0.3114	0.0885	0.2021	-20.6247	-51.4242	18.7857
26	0.1837	-0.2411	0.2163	0.7092	0.183	1.0724	0.3927	0.2541	0.2257	0.0205	0.0878	-0.2142	-0.5054	-0.7649	0.5186	0.1756	0.0393	-0.0066	0.3158	0.052	0.0728	-19.2796	-47.7591	-5.5333
27	0.4417	-0.0906	0.2621	0.2241	-0.3293	0.4783	-0.0779	0.1098	-0.038	0.0948	0.091	-0.1406	0.0143	-0.3044	0.028	0.1722	-0.0088	-0.0011	0.122	0.025	0.1798	-9.4217	-49.9389	-0.4406
28	0.7382	-0.1205	-1.1189	0.4308	0.1238	1.6577	-0.6127	0.2252	-0.1311	0.0352	-0.1128	-0.1308	0.3542	-0.4327	-0.5902	0.1085	0.105	-0.0917	-0.0398	0.1828	0.2239	-11.5062	-57.6073	8.2497
29	0.0603	0.1549	0.0616	0.1484	0.0175	0.4236	-0.0038	-0.0013	-0.0234	-0.0438	-0.0314	-0.1605	0.3135	-0.2238	-0.0228	0.1408	-0.0028	0.0035	0.1121	0.0198	0.1651	-10.9526	-59.5709	-8.0715
30	0.2039	-0.0036	-0.1019	0.1903	0.2732	0.2829	0.0906	0.167	-0.1815	-0.1104	0.1216	0.1053	0.0314	-0.6654	0.033	0.1877	-0.0807	0.0297	0.3927	0.0107	0.2499	-24.9122	-54.841	-10.7066

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:20)
2	X-RAY DIFFRACTION	2	(chain A and resid 21:28)
3	X-RAY DIFFRACTION	3	(chain A and resid 29:52)
4	X-RAY DIFFRACTION	4	(chain A and resid 53:69)
5	X-RAY DIFFRACTION	5	(chain A and resid 70:91)
6	X-RAY DIFFRACTION	6	(chain A and resid 92:131)
7	X-RAY DIFFRACTION	7	(chain A and resid 132:186)
8	X-RAY DIFFRACTION	8	(chain A and resid 187:194)
9	X-RAY DIFFRACTION	9	(chain A and resid 195:239)
10	X-RAY DIFFRACTION	10	(chain A and resid 240:251)
11	X-RAY DIFFRACTION	11	(chain A and resid 252:291)
12	X-RAY DIFFRACTION	12	(chain A and resid 292:327)
13	X-RAY DIFFRACTION	13	(chain A and resid 328:340)
14	X-RAY DIFFRACTION	14	(chain A and resid 341:375)
15	X-RAY DIFFRACTION	15	(chain A and resid 376:400)
16	X-RAY DIFFRACTION	16	(chain B and resid 2:20)
17	X-RAY DIFFRACTION	17	(chain B and resid 21:28)
18	X-RAY DIFFRACTION	18	(chain B and resid 29:52)
19	X-RAY DIFFRACTION	19	(chain B and resid 53:69)
20	X-RAY DIFFRACTION	20	(chain B and resid 70:91)
21	X-RAY DIFFRACTION	21	(chain B and resid 92:131)
22	X-RAY DIFFRACTION	22	(chain B and resid 132:186)
23	X-RAY DIFFRACTION	23	(chain B and resid 187:194)
24	X-RAY DIFFRACTION	24	(chain B and resid 195:239)
25	X-RAY DIFFRACTION	25	(chain B and resid 240:251)
26	X-RAY DIFFRACTION	26	(chain B and resid 252:291)
27	X-RAY DIFFRACTION	27	(chain B and resid 292:327)
28	X-RAY DIFFRACTION	28	(chain B and resid 328:340)
29	X-RAY DIFFRACTION	29	(chain B and resid 341:375)
30	X-RAY DIFFRACTION	30	(chain B and resid 376:400)

-
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://pdbjlvh1.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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 792 molecules

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 792 molecules

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 792 molecules

-
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