PDB-7nny: Crystal structure of Mycobacterium tuberculosis ArgF in complex w...

ID or keywords:

Entry

Database: PDB / ID: 7nny

Title

Crystal structure of Mycobacterium tuberculosis ArgF in complex with naphthalen-1-ol.

Components

Ornithine carbamoyltransferase

Ornithine transcarbamylase

Keywords

TRANSFERASE / ArgF /

Ornithine Carbamoyltransferase

Function / homology

Function and homology information

ornithine carbamoyltransferase /

ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / arginine biosynthetic process /

amino acid binding /

cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.57 Å

Authors

Mendes, V. / Gupta, P. / Burgess, A. / Sebastian-Perez, V. / Cattermole, E. / Meghir, C. / Blundell, T.L.

Funding support

United States, 1items

Citation

Journal: Comput Struct Biotechnol J / Year: 2021
Title: A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis
Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / ...

History

Deposition	Feb 25, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 30, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7nny.cif.gz	712.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7nny.ent.gz	589.5 KB	Display	PDB format
PDBx/mmJSON format	7nny.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nn/7nny ftp://data.pdbj.org/pub/pdb/validation_reports/nn/7nny	HTTPS FTP

-
Related structure data

Related structure data	7nlfC 7nlnC 7nloC 7nlpC 7nlqC 7nlrC 7nlsC 7nltC 7nluC 7nlwC 7nlxC 7nlyC 7nlzC 7nm0C 7nn1C 7nn4C 7nn7C 7nn8C 7nnbC 7nncC 7nnfC 7nniC 7nnqC 7nnrC 7nnvC 7nnwC 7nnzC 7norC 7nosC 7notC 7nouC 7novC 7np0C 7nphC 7npjC 2p2gS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7nnz-1 7nnz-2 2p2g-2 7nnv-1 7nor-1 7nnf-2 7nov-1 7nnf-1 7np0-2 2p2g-1 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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (7)

Deposited unit

A: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

C: Ornithine carbamoyltransferase

D: Ornithine carbamoyltransferase

E: Ornithine carbamoyltransferase

F: Ornithine carbamoyltransferase

hetero molecules

202 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

C: Ornithine carbamoyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
101 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Ornithine carbamoyltransferase

E: Ornithine carbamoyltransferase

F: Ornithine carbamoyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.947, 143.785, 97.278
Angle α, β, γ (deg.)	90.000, 117.600, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ornithine carbamoyltransferase / Ornithine transcarbamylase / OTCase Mass: 33208.324 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: argF, Rv1656, MTCY06H11.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIT9, ornithine carbamoyltransferase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-1NP / 1-NAPHTHOL / naphthalen-1-ol / 1-Naphthol Mass: 144.170 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₀H₈O / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1772 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion Details: 150 mM ammonium dihydrogen phosphate 10 mM praseodymium acetate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.57→86.21 Å / Num. obs: 294032 / % possible obs: 94.6 % / Redundancy: 4.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.048 / R_pim(I) all: 0.023 / R_rim(I) all: 0.054 / Net I/σ(I): 15.4 / Num. measured all: 1448621 / Scaling rejects: 11

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.57-1.66	3.3	1.072	105414	31609	0.424	0.632	1.255	0.9	69.8
4.97-86.21	5.1	0.024	51326	9979	0.999	0.011	0.027	52.6	99.8

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	8.03 Å	86.21 Å

-
Processing

Software

Name	Version	Classification
Aimless	0.7.1	data scaling
PHASER	2.8.3	phasing
PHENIX	1.18.2	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2P2G

2p2g

Resolution: 1.57→48.97 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1842	14812	5.04 %
R_work	0.1661	279122	-
obs	0.167	293934	94.55 %

Solvent computation

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

Displacement parameters

B_iso max: 82.99 Å² / B_iso mean: 30.999 Å² / B_iso min: 16.37 Å²

Refinement step

Cycle: final / Resolution: 1.57→48.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13664	0	187	1776	15627
B_iso mean	-	-	40.72	40.41	-
Num. residues	-	-	-	-	1809

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.57-1.59	0.3351	327	0.3235	6022	6349	61
1.59-1.61	0.3261	352	0.3031	6454	6806	66
1.61-1.63	0.3165	345	0.2877	7073	7418	72
1.63-1.65	0.3048	417	0.277	7434	7851	76
1.65-1.67	0.2745	423	0.2608	8011	8434	81
1.67-1.69	0.2591	446	0.2487	8528	8974	87
1.69-1.72	0.2713	486	0.2397	9237	9723	94
1.72-1.74	0.2547	482	0.2262	9870	10352	100
1.74-1.77	0.2382	496	0.218	9823	10319	100
1.77-1.8	0.2278	524	0.2069	9842	10366	100
1.8-1.83	0.2449	501	0.2093	9829	10330	100
1.83-1.86	0.2189	503	0.1923	9796	10299	100
1.86-1.9	0.2188	504	0.1766	9853	10357	100
1.9-1.94	0.2059	541	0.1754	9788	10329	100
1.94-1.98	0.192	513	0.1787	9840	10353	100
1.98-2.02	0.2013	522	0.1695	9853	10375	100
2.02-2.07	0.1987	478	0.17	9858	10336	100
2.07-2.13	0.1887	484	0.1617	9874	10358	100
2.13-2.19	0.1756	539	0.158	9760	10299	100
2.19-2.26	0.1753	557	0.1593	9843	10400	100
2.26-2.35	0.1747	532	0.1626	9804	10336	100
2.35-2.44	0.188	526	0.1602	9848	10374	100
2.44-2.55	0.1993	500	0.1589	9860	10360	100
2.55-2.68	0.18	548	0.162	9810	10358	100
2.68-2.85	0.1868	586	0.168	9798	10384	100
2.85-3.07	0.1763	512	0.1631	9866	10378	100
3.07-3.38	0.1755	543	0.1617	9858	10401	100
3.38-3.87	0.1778	466	0.1512	9937	10403	100
3.87-4.88	0.1446	549	0.1373	9869	10418	100
4.88-48.97	0.1689	610	0.1608	9884	10494	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	0.9358	-0.6676	-0.1218	1.0536	-0.0332	0.7103	-0.0149	-0.0446	0.0718	0.0561	0.012	0.0194	-0.0419	0.032	0	0.1701	-0.008	-0.0169	0.1792	-0.0174	0.195	0.1876	-4.4751	-41.4704
2	0.8287	-0.9596	-0.0195	1.1164	-0.1719	0.4355	0.0971	0.0951	0.0467	-0.1842	-0.1008	-0.0652	-0.0234	0.0314	-0.0001	0.2109	0.0015	-0.0101	0.2135	-0.0109	0.1983	0.7408	-1.9119	-51.9972
3	0.3224	0.2782	-0.1954	0.4355	0.2186	0.3595	-0.062	-0.016	-0.0319	-0.051	0.0666	-0.0944	0.019	0.1703	-0	0.1785	0.0186	-0.0018	0.2538	-0.01	0.2113	15.0344	-19.494	-49.7466
4	0.4746	0.0619	-0.3954	0.9803	0.0616	1.5482	-0.0686	0.0169	-0.0397	-0.0916	0.0819	-0.0901	0.095	0.026	0	0.1691	0.0207	0.0189	0.206	-0.0011	0.2373	13.7157	-22.2025	-55.0518
5	0.7281	0.1541	-0.311	0.5917	0.269	0.4082	-0.17	-0.0599	-0.1551	0.1038	0.012	0.0968	0.1963	-0.0496	-0.0001	0.2692	0.0041	0.0298	0.218	0.0123	0.2429	4.3853	-31.0447	-47.0104
6	0.4531	-0.3698	-0.2738	0.2999	-0.0341	0.5056	-0.022	-0.0986	0.0402	0.0849	0.0074	0.0319	-0.0087	0.0167	-0	0.1857	-0.0095	-0.0036	0.2197	-0.009	0.2088	1.2162	-8.6508	-39.4904
7	1.6595	0.3251	0.3841	0.9187	0.3027	0.7665	-0.0023	-0.0039	-0.0016	0.0595	-0.0694	0.1072	0.0214	0.0089	-0.0001	0.1709	0.0008	0.0019	0.2051	-0.0102	0.2219	-28.0244	-13.575	-38.7
8	0.5354	0.0256	-0.3769	0.4843	-0.1582	0.0666	-0.0559	0.1812	-0.1273	-0.3483	0.0997	0.0124	-0.0058	-0.0576	0.0002	0.2578	-0.0274	0.0108	0.3148	-0.0377	0.2514	-12.9342	-18.5396	-48.661
9	1.6565	0.3177	0.5466	0.8011	0.2601	0.7088	-0.0367	0.2044	-0.1971	-0.018	-0.0283	0.1905	0.1044	-0.0215	-0.0058	0.1715	-0.0196	0.0126	0.2261	-0.0712	0.3127	-39.3044	-23.6243	-46.1744
10	0.8507	0.5271	0.5124	0.8875	0.0734	0.6635	-0.2062	0.2386	0.1511	-0.2344	0.0358	0.463	-0.1474	-0.1479	-0.4364	0.2293	-0.0245	-0.1317	0.3653	-0.0258	0.456	-50.2182	-12.5723	-54.5687
11	0.3522	0.4561	0.137	0.4711	0.2056	0.2218	0.0013	-0.0254	0.05	0.0982	-0.0463	0.274	-0.0111	-0.0349	0.0003	0.1831	-0.0006	0.011	0.2099	-0.0121	0.2875	-32.3727	-12.0516	-38.3563
12	0.5368	0.1294	-0.2463	0.8267	-0.0177	0.9659	0.0492	-0.0069	-0.0297	0.0137	-0.0461	0.1168	-0.0984	-0.0507	-0	0.2024	0.0137	-0.0205	0.2117	-0.0192	0.2151	-22.083	14.0091	-47.4876
13	0.3012	0.3853	-0.3021	1.0936	-0.3807	0.7004	-0.0331	0.1325	0.0069	-0.1498	0.0449	0.1718	-0.0119	-0.1284	-0	0.2351	0.0107	-0.0474	0.2608	-0.0161	0.2671	-27.8463	9.1946	-55.2756
14	1.1442	0.0002	-0.425	0.5215	-0.5688	1.2754	0.0372	0.2259	0.1235	-0.1301	0.0147	0.131	-0.3038	-0.1639	0	0.3843	0.0427	-0.0406	0.2554	0.0137	0.2348	-20.0461	28.478	-66.092
15	0.7247	0.0537	-0.0959	0.5329	-0.7567	0.778	0.0131	0.1189	-0.0353	-0.0618	-0.0079	-0.042	-0.0592	0.2974	-0	0.3246	-0.007	-0.0017	0.2753	0.0194	0.2234	-7.131	22.4725	-69.584
16	0.1768	0.1207	0.2688	0.3896	-0.1556	0.448	0.0475	0.0378	-0.0014	0.0209	-0.0528	0.0326	-0.2267	-0.0225	0.0001	0.2345	0.0177	-0.0148	0.2148	-0.0131	0.2151	-18.7498	17.167	-47.9466
17	1.1257	-0.4898	-0.0622	0.9106	0.1115	0.6939	-0.0663	-0.0107	-0.0084	0.0713	0.0944	-0.0332	-0.0162	-0.0236	-0	0.2153	0.0294	0.0132	0.2164	0.017	0.1749	-21.8857	21.86	-21.7128
18	1.1672	-0.9797	0.3983	0.7903	-0.1202	0.3734	-0.1528	-0.1779	0.1267	0.1886	0.176	-0.0516	-0.0523	-0.051	0.0006	0.2652	0.0643	-0.0173	0.2395	-0.0201	0.1945	-16.3553	25.9305	-13.3685
19	0.6791	-0.2119	-0.1819	0.463	0.2002	0.1743	-0.0443	-0.0512	0.1198	0.0522	0.1286	0.0162	-0.1113	-0.0144	-0.0001	0.2862	0.0936	0.0259	0.2517	0.0237	0.2099	-35.4545	38.0278	-13.6277
20	0.1842	-0.3155	0.0252	0.6045	0.3188	0.3666	-0.0225	-0.018	0.3364	0.0501	0.156	-0.0034	-0.313	-0.0349	0.0001	0.3271	0.0642	0.0375	0.2508	0.0174	0.3226	-34.9771	44.4893	-16.0271
21	0.4323	-0.0163	-0.088	0.963	0.4726	0.3017	-0.1448	-0.1405	-0.0657	0.29	0.1619	0.2482	0.0472	0.0142	-0.0033	0.3296	0.116	0.1056	0.2984	0.0764	0.2513	-44.0874	29.1631	-7.3881
22	0.192	-0.2432	0.0235	0.3355	0.1645	0.2843	0.0274	0.0161	-0.047	0.0611	0.0594	0.0156	-0.0517	-0.0236	0.0001	0.2487	0.0365	0.0314	0.226	0.0196	0.2129	-26.6353	22.0073	-22.4293
23	0.4142	0.1435	-0.0465	1.1008	-0.6771	1.193	-0.0403	0.0801	0.0075	-0.0474	0.0076	-0.0105	0.051	-0.1592	-0	0.2163	-0.011	-0.0036	0.2232	-0.0078	0.1963	-27.0507	-6.1304	-12.8517
24	0.4095	-0.1189	-0.1963	0.7183	-0.241	0.1164	0.0317	-0.1262	0.0279	0.3	0.0556	-0.1316	-0.2196	-0.0488	-0.0008	0.3621	0.0491	0.0087	0.2742	0.0285	0.201	-31.5771	11.2094	-6.5419
25	0.2292	0.6108	-0.3003	0.7876	-0.7203	0.7579	0.0433	0.0114	-0.0187	0.1852	-0.0452	0.1705	-0.0416	-0.1379	0	0.2584	-0.003	0.0239	0.2376	-0.0149	0.2159	-31.1119	-5.8387	-4.5372
26	0.3715	-0.0421	-0.1126	0.1283	-0.2546	0.2744	-0.0692	0.0065	-0.092	0.1035	-0.0025	-0.0445	0.2777	-0.2648	-0.0002	0.3261	-0.063	0.0462	0.2201	-0.0193	0.2555	-28.671	-23.2164	1.9666
27	0.4136	-0.0597	-0.0436	0.0404	-0.0474	0.1629	-0.0571	-0.0459	-0.0295	0.0343	0.0364	0.107	0.0468	-0.1595	0	0.2909	-0.0579	0.0293	0.2526	-0.0123	0.2371	-32.7528	-18.6454	5.472
28	0.3136	-0.2261	0.4874	0.3628	-0.1456	1.0038	-0.1454	0.077	-0.1373	0.1043	0.2993	0.4534	0.1952	-0.8559	0.0347	0.3096	-0.1072	0.0152	0.4151	0.0214	0.3089	-42.4444	-19.8641	1.3382
29	0.8885	-0.3142	-0.4572	0.4088	-0.4099	0.8257	-0.085	-0.2297	-0.0873	-0.0348	0.043	-0.111	0.1548	0.0328	0	0.3048	-0.0177	0.0321	0.2207	0.0075	0.2457	-24.8597	-20.9559	12.2162
30	0.3539	0.2131	-0.102	0.3263	-0.471	0.6576	-0.1129	-0.0561	-0.0851	-0.0595	-0.0496	-0.0807	0.1694	0.3051	-0.0003	0.3241	0.0283	0.0511	0.243	0.0302	0.2885	-15.5979	-22.7714	5.5357
31	0.2395	0.0437	-0.2974	0.2596	-0.1245	0.3569	-0.0305	0.0491	-0.0266	-0.1583	-0.0036	-0.037	0.1574	-0.125	0.0002	0.2385	-0.0283	0.0167	0.2453	-0.0064	0.2372	-25.0974	-10.2737	-12.4283
32	1.2235	0.1614	-0.0074	0.7635	0.0674	0.7075	-0.0666	0.0552	-0.1516	-0.0228	0.0613	-0.0874	0.022	0.0586	-0	0.2056	0.0023	0.0068	0.1789	-0.0076	0.2144	2.7306	1.8434	-16.6644
33	0.2156	0.3545	0.2394	0.4816	0.0328	0.0368	-0.043	-0.0909	0.003	0.1417	-0.0334	0.0694	-0.0314	-0.1608	0	0.2508	0.0198	0.0219	0.2489	-0.0052	0.2211	-8.2289	4.727	-6.7104
34	1.1623	0.3554	-0.0776	0.0958	0.0791	0.5548	-0.0269	-0.1756	-0.067	0.0534	-0.0364	-0.0626	-0.0035	0.0774	0	0.2442	0.009	-0.0017	0.2382	0.0165	0.2307	2.316	1.107	-7.0445
35	0.1942	0.0229	0.3143	0.2409	-0.1298	0.2442	-0.0192	-0.029	0.0061	0.0748	0.0218	-0.0645	-0.0133	0.3184	0.0018	0.2921	-0.0502	-0.0064	0.3252	-0.0254	0.2903	19.3614	15.4309	-10.0998
36	0.9143	0.1038	0.7399	0.8108	-0.0413	0.9076	-0.0852	-0.0754	-0.0739	0.1255	0.0459	-0.1747	-0.1434	0.1092	0.0003	0.2903	-0.0257	-0.0374	0.2821	-0.0089	0.2771	19.8658	14.4942	-3.7141
37	0.505	0.0809	0.4901	0.5421	0.108	0.3226	-0.2524	-0.0039	0.2059	0.0171	0.0335	0.0155	-0.2816	0.0019	-0	0.3954	-0.0375	-0.0732	0.2424	-0.0069	0.3249	12.9155	27.5897	-9.8575
38	0.586	0.1259	0.3306	0.0859	-0.0878	0.5403	-0.1407	0.0905	-0.0037	-0.0138	0.208	0.0112	-0.0783	0.0139	0.0002	0.2314	0.0042	-0.0044	0.214	-0.0089	0.2319	3.221	7.2888	-17.8273

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 0 through 64 )	A	0 - 64
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 65 through 143 )	A	65 - 143
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 144 through 187 )	A	144 - 187
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 188 through 245 )	A	188 - 245
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 246 through 284 )	A	246 - 284
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 285 through 307 )	A	285 - 307
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 64 )	B	1 - 64
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 65 through 94 )	B	65 - 94
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 95 through 215 )	B	95 - 215
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 216 through 284 )	B	216 - 284
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 285 through 307 )	B	285 - 307
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 64 )	C	1 - 64
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 65 through 143 )	C	65 - 143
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 144 through 231 )	C	144 - 231
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 232 through 284 )	C	232 - 284
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 285 through 307 )	C	285 - 307
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 0 through 64 )	D	0 - 64
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 65 through 143 )	D	65 - 143
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 144 through 187 )	D	144 - 187
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 188 through 215 )	D	188 - 215
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 216 through 284 )	D	216 - 284
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 285 through 307 )	D	285 - 307
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 1 through 64 )	E	1 - 64
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 65 through 94 )	E	65 - 94
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 95 through 143 )	E	95 - 143
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 144 through 159 )	E	144 - 159
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 160 through 187 )	E	160 - 187
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 188 through 201 )	E	188 - 201
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 202 through 245 )	E	202 - 245
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 246 through 284 )	E	246 - 284
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 285 through 307 )	E	285 - 307
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 0 through 50 )	F	0 - 50
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 51 through 83 )	F	51 - 83
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 84 through 143 )	F	84 - 143
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 144 through 159 )	F	144 - 159
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 160 through 245 )	F	160 - 245
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 246 through 284 )	F	246 - 284
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 285 through 307 )	F	285 - 307

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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