PDB-6thc: Crystal structure of Mycobacterium smegmatis CoaB in complex with...

ID or keywords:

Entry

Database: PDB / ID: 6thc

Title

Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP and (4-hydroxyphenyl)(2,3,4-trihydroxyphenyl)methanone

Components

Coenzyme A biosynthesis bifunctional protein CoaBC

Keywords

LIGASE / CoaBC / bifunctional Phosphopantothenoylcysteine decarboxylase/phosphopantothenate-cysteine ligase / phosphopantothenate-cysteine ligase / Phosphopantothenoylcysteine decarboxylase / phosphopantothenoylcysteine synthetase

Function / homology

Function and homology information

pantothenate catabolic process / phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / coenzyme A biosynthetic process / FMN binding / metal ion binding
Similarity search - Function

Biological species

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.033 Å

Authors

Mendes, V. / Blaszczyk, M. / Bryant, O. / Cory-Wright, J. / Blundell, T.L.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2021
Title: Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site.
Authors: Mendes, V. / Green, S.R. / Evans, J.C. / Hess, J. / Blaszczyk, M. / Spry, C. / Bryant, O. / Cory-Wright, J. / Chan, D.S. / Torres, P.H.M. / Wang, Z. / Nahiyaan, N. / O'Neill, S. / Damerow, S. ...

History

Deposition	Nov 19, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 20, 2021	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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 24, 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	6thc.cif.gz	344.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6thc.ent.gz	280.2 KB	Display	PDB format
PDBx/mmJSON format	6thc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6thc_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	6thc_full_validation.pdf.gz	2.9 MB	Display
Data in XML	6thc_validation.xml.gz	36.5 KB	Display
Data in CIF	6thc_validation.cif.gz	50.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/th/6thc ftp://data.pdbj.org/pub/pdb/validation_reports/th/6thc	HTTPS FTP

-
Related structure data

Related structure data	6tgvC 6th2C 4qjiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4p93-d 3srx-d 6th2-1 3nwj-d 4qji-3 5oe9-3 2a70-d 1pii-d 6th2-2 3rkj-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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1)

Deposited unit

A: Coenzyme A biosynthesis bifunctional protein CoaBC

B: Coenzyme A biosynthesis bifunctional protein CoaBC

C: Coenzyme A biosynthesis bifunctional protein CoaBC

D: Coenzyme A biosynthesis bifunctional protein CoaBC

hetero molecules

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

1

A: Coenzyme A biosynthesis bifunctional protein CoaBC

B: Coenzyme A biosynthesis bifunctional protein CoaBC

hetero molecules

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

2

C: Coenzyme A biosynthesis bifunctional protein CoaBC

D: Coenzyme A biosynthesis bifunctional protein CoaBC

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.010, 77.371, 144.351
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Coenzyme A biosynthesis bifunctional protein CoaBC / DNA/pantothenate metabolism flavoprotein Mass: 24773.990 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: coaBC, MSMEG_3054 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0QWT2, phosphopantothenoylcysteine decarboxylase, phosphopantothenate-cysteine ligase (CTP)

#1: Protein

Coenzyme A biosynthesis bifunctional protein CoaBC / DNA/pantothenate metabolism flavoprotein

Mass: 24773.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycolicibacterium smegmatis (bacteria) / Gene: coaBC, MSMEG_3054 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0QWT2, phosphopantothenoylcysteine decarboxylase, phosphopantothenate-cysteine ligase (CTP)

-
Non-polymers , 5 types, 309 molecules

#2: Chemical	ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-N9N / (4-hydroxyphenyl)-[2,3,4-tris(oxidanyl)phenyl]methanone Mass: 246.215 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₃H₁₀O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.57 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% w/v PEG 8000 0.1M MES pH 6.0 0.2M calcium acetate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97626 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.97626 Å / Relative weight: 1

Reflection

Resolution: 2.03→77.37 Å / Num. obs: 55496 / % possible obs: 99.9 % / Redundancy: 6.5 % / B_iso Wilson estimate: 35.46 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.093 / R_pim(I) all: 0.04 / R_rim(I) all: 0.101 / Net I/σ(I): 13.1 / Num. measured all: 360758 / Scaling rejects: 488

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
2.03-2.14	6.7	0.846	53437	7959	0.738	0.354	0.919	2.4	100
6.43-77.37	5.7	0.046	11000	1928	0.998	0.02	0.05	31.9	99.4

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	5.8 Å	72.18 Å
Translation	5.8 Å	72.18 Å

-
Processing

Software

Name	Version	Classification
PHENIX	1.14	refinement
Aimless	0.5.15	data scaling
PHASER	2.6.0	phasing
PDB_EXTRACT	3.25	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4QJI

4qji

Resolution: 2.033→72.176 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.88

	R_factor	Num. reflection	% reflection
R_free	0.2407	2792	5.04 %
R_work	0.1841	-	-
obs	0.187	55419	99.9 %

Solvent computation

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

Displacement parameters

B_iso max: 136.75 Å² / B_iso mean: 48.9335 Å² / B_iso min: 18.8 Å²

Refinement step

Cycle: final / Resolution: 2.033→72.176 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6220	0	240	292	6752
B_iso mean	-	-	55.07	46.36	-
Num. residues	-	-	-	-	874

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6536
X-RAY DIFFRACTION	f_angle_d	0.977	8893
X-RAY DIFFRACTION	f_chiral_restr	0.062	1046
X-RAY DIFFRACTION	f_plane_restr	0.005	1155
X-RAY DIFFRACTION	f_dihedral_angle_d	19.659	3851

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 (%)
2.0333-2.0684	0.3229	116	0.2707	2579	100
2.0684-2.106	0.3223	136	0.2606	2615	100
2.106-2.1465	0.3109	142	0.2412	2583	100
2.1465-2.1903	0.2843	119	0.2316	2610	100
2.1903-2.2379	0.2714	135	0.2181	2607	100
2.2379-2.29	0.2573	116	0.2082	2630	100
2.29-2.3473	0.2649	141	0.204	2609	100
2.3473-2.4107	0.2549	152	0.2053	2605	100
2.4107-2.4817	0.2571	155	0.2071	2568	100
2.4817-2.5618	0.3027	153	0.2033	2582	100
2.5618-2.6533	0.2773	155	0.2058	2642	100
2.6533-2.7596	0.2847	136	0.2002	2608	100
2.7596-2.8852	0.2588	160	0.1999	2593	100
2.8852-3.0373	0.2696	128	0.1959	2657	100
3.0373-3.2276	0.2304	139	0.1892	2644	100
3.2276-3.4768	0.2273	136	0.1748	2651	100
3.4768-3.8267	0.1951	132	0.153	2665	100
3.8267-4.3803	0.1852	134	0.1504	2670	100
4.3803-5.5185	0.2062	129	0.1546	2719	100
5.5185-72.176	0.2509	178	0.1857	2790	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	2.8842	-0.0939	2.0124	2.0791	-0.1241	3.6498	0.2849	-0.3871	-0.1793	-0.0014	-0.1696	-0.0671	0.7214	0.0132	-0.0594	0.4812	0	-0.0515	0.14	-0.0067	0.2096	74.7427	22.3646	30.663
2	5.0911	3.5627	-0.3149	6.7088	-2.5225	3.8674	0.5396	0.3623	-1.0137	0.1915	-0.0117	-0.2786	1.4459	0.0418	-0.3201	0.8259	-0.0025	-0.1605	0.2438	-0.0022	0.3663	68.8202	15.1156	31.493
3	3.3909	1.4733	4.2808	3.9526	0.9732	5.7772	-0.1146	1.1011	0.2059	-0.7639	0.255	0.2222	0.1117	0.545	-0.1859	0.458	0.0092	-0.0672	0.4284	-0.0324	0.1989	69.3136	25.4993	20.5403
4	1.9758	0.7904	0.1813	1.8291	0.0004	2.1903	0.1946	0.2846	0.2462	0.1646	-0.1882	-0.3036	-0.0375	0.3334	0.0922	0.3956	0.0218	-0.0742	0.2593	0.0868	0.2765	82.8636	31.2349	26.4532
5	7.0007	-0.4697	1.2781	-0.0149	0.1096	1.4024	-0.0351	0.3699	0.7409	0.0876	-0.1883	-0.0641	-0.0783	0.2399	0.1344	0.3833	0.0245	-0.0766	0.2181	0.0226	0.2958	68.2793	35.7838	25.4723
6	1.909	0.6812	1.607	1.9945	1.2436	4.3387	0.0819	0.0593	0.1741	0.1575	0.0019	0.0398	0.0097	0.3241	-0.0024	0.3242	0.0467	0.0065	0.2909	-0.0273	0.22	63.4948	35.8468	36.8557
7	3.4174	2.8217	-0.0073	3.7084	2.56	7.3385	0.3554	0.276	-0.3759	0.1715	0.1798	-0.3366	0.2649	0.1708	-0.162	0.4069	0.0075	-0.0137	0.3301	-0.046	0.2952	62.3671	30.7431	42.3243
8	4.3611	-1.1758	-0.8787	1.9535	-0.2502	6.0828	-0.0613	-0.7874	-0.5326	0.7901	0.655	0.292	-0.0103	-0.2877	-0.428	0.4554	0.0294	-0.0423	0.4102	-0.0094	0.4726	58.81	27.8495	46.1771
9	2.8619	-5.1896	1.3757	9.7943	-2.8835	6.9073	-0.6656	-0.6399	-0.6102	1.3574	0.4961	0.4378	-0.2866	-0.717	0.0368	0.635	-0.1416	0.0749	0.4695	0.0631	0.4548	56.8068	20.9906	39.9065
10	6.1093	1.9667	1.87	6.6533	-2.2749	2.1846	0.0667	0.206	-0.8261	0.1785	-0.1284	-0.8437	0.4347	0.2891	-0.0508	0.4385	0.015	-0.115	0.3415	-0.0274	0.4811	106.7485	5.2435	44.5207
11	5.2112	-3.046	0.5297	5.8411	1.1585	2.879	0.0097	0.2585	0.0981	0.0956	-0.3058	0.1512	-0.2015	-0.3042	0.1904	0.2706	-0.0379	-0.0672	0.3538	0.0548	0.2654	88.8663	26.5431	36.6856
12	3.0375	-0.4385	0.7296	4.9188	0.425	1.6324	-0.0681	-0.1821	0.0128	0.3152	0.056	-0.0709	0.0592	-0.2414	0.0134	0.262	-0.031	-0.0563	0.2812	-0.0012	0.1808	99.4286	13.7558	43.4751
13	8.3258	-3.9463	0.3565	4.7069	0.2188	2.2308	-0.3036	-0.0562	1.753	-0.1195	0.0515	-0.4734	-0.4686	-0.0742	0.3038	0.451	-0.0494	-0.0852	0.3088	0.0322	0.5322	96.0863	34.498	37.9669
14	4.1176	0.4396	2.1009	5.8487	2.6764	8.8925	-0.3316	0.9198	0.4496	-1.0243	0.6323	-0.3759	-0.8242	1.0055	-0.1246	0.4062	-0.2015	0.0063	0.6176	0.0388	0.543	112.5576	18.4324	33.7683
15	5.2032	2.8661	6.1223	1.584	3.4353	7.1525	1.1446	-1.3562	-0.4381	0.1933	-0.4885	-0.0566	0.7177	-0.9247	-0.6063	0.5177	-0.084	-0.1282	0.655	0.0533	0.5933	101.3307	11.6058	26.3265
16	7.5927	3.5609	-0.0899	7.1099	0.3452	7.3925	0.0539	1.281	-0.0903	-0.6211	0.5861	-0.6876	0.4906	0.5615	-0.3811	0.3781	0.0402	0.1289	0.5655	-0.1108	0.443	108.9564	7.0377	28.9527
17	3.0669	0.2934	0.5019	7.0083	-0.8298	2.8373	0.1549	-0.2066	-0.3227	-0.3822	-0.0061	1.093	0.5846	-0.3874	-0.147	0.3071	-0.0496	-0.0572	0.3785	0.0494	0.3751	72.6678	0.2566	5.3715
18	0.2444	-1.0805	0.1213	5.3713	-0.1099	2.7142	-0.0465	-0.1108	0.1224	0.1935	0.065	-0.2399	0.0057	0.0685	0.0851	0.1651	-0.0091	-0.0048	0.2843	0.0383	0.2694	82.7511	27.433	4.917
19	5.6678	2.7113	0.2176	2.1822	0.6144	3.8912	-0.0675	0.281	-0.3125	-0.1595	0.0511	0.2047	0.2808	-0.5569	0.0712	0.2053	-0.0223	-0.0104	0.3727	0.0075	0.2818	71.5826	6.8407	2.111
20	5.1138	2.3687	0.8734	4.9095	1.3332	2.3026	-0.1584	0.1496	0.7702	-0.1091	0.2382	1.0964	-0.031	-0.5337	0.0739	0.2454	0.025	-0.0291	0.3825	0.0674	0.4655	71.3722	16.2679	6.1656
21	3.8563	0.5841	-0.0647	2.097	-0.7311	4.2993	-0.055	-0.5355	0.0804	1.0576	-0.0436	0.1483	-0.1503	0.1671	0.0521	0.2954	0.0231	0.0133	0.3568	0.0272	0.1723	81.4678	11.6886	15.37
22	2.2712	1.6536	0.2956	2.8079	0.1099	1.9889	-0.3027	0.1476	0.1329	-0.0485	0.262	-0.2944	-0.2282	0.2391	0.0337	0.1509	0.0268	-0.0339	0.3439	0.0673	0.2573	87.963	23.2176	9.0851
23	0.1125	-0.3356	0.0677	2.8902	-2.4254	2.0561	-0.1411	-0.0551	0.0032	0.2479	-0.1439	-0.7746	-0.0013	0.1326	0.2482	0.1931	0.0708	0.0231	0.359	0.0729	0.3034	92.0074	10.5226	10.5042
24	4.9129	2.0037	-3.5736	4.4122	-2.5854	6.2281	-0.0445	0.0391	-0.1468	-0.0291	0.1121	-0.161	-0.0403	0.1428	-0.0531	0.2089	-0.0094	0.0094	0.1834	-0.0534	0.1833	89.5278	5.1473	2.0973
25	4.877	1.9728	-4.0004	4.87	-4.511	6.0993	0.0041	0.3528	-0.4982	-0.2421	0.0638	-0.3175	0.3205	0.3794	0.1286	0.2111	0.0011	0.0322	0.3477	0.0048	0.182	96.1759	6.2685	-4.8214
26	8.8432	1.6205	-1.8294	3.3195	3.0025	4.0691	-0.2429	0.7223	0.3701	-0.5906	0.2023	0.1616	-0.0565	-0.4767	-0.2097	0.3031	0.0232	0.0321	0.3659	0.0412	0.2455	87.3039	4.7271	-6.647
27	7.6758	1.9751	-1.1054	7.0709	3.2787	5.0083	-0.1272	0.7999	0.5989	-0.5889	0.2511	1.0716	-0.1088	-0.608	0.1374	0.4193	-0.0534	-0.004	0.4133	-0.0094	0.393	85.2781	0.2231	-9.8919
28	2.8243	-2.7734	3.2288	3.5514	-4.9766	9.6731	0.4795	0.965	-0.3338	-1.227	-0.1125	-0.5018	1.0658	0.1618	-0.583	0.4198	-0.0182	-0.0544	0.4592	-0.1155	0.5395	77.8974	-1.7714	-3.7684
29	1.104	-0.8054	0.6004	3.3026	-1.7853	2.4282	-0.1161	-0.166	0.1086	-0.0219	0.2248	0.1042	-0.0835	-0.1238	-0.07	0.2185	-0.0765	-0.0241	0.2452	0.0531	0.3104	75.592	38.58	-3.9847
30	8.6739	-0.979	-2.1021	2.9533	1.3745	3.153	0.0466	0.2668	-0.308	-0.1347	-0.0326	0.1692	0.1647	-0.2712	0.0511	0.2394	-0.0472	-0.0336	0.2547	0.0706	0.3103	66.731	40.0439	-7.0653
31	3.2422	-2.0451	0.1362	5.065	-0.8208	1.8357	-0.1129	0.0898	0.3367	-0.0741	-0.0457	-0.6268	0.0376	0.2919	0.1763	0.227	-0.0746	0.02	0.2916	0.0396	0.3097	86.9426	38.6891	-4.942
32	3.8045	-0.2971	-1.0983	3.1481	-1.122	6.1267	0.1648	-0.3229	0.6358	0.8864	-0.1825	-0.4532	-1.0741	0.546	0.1637	0.5397	-0.114	-0.0782	0.2583	-0.0135	0.5179	77.8822	55.1439	0.6251
33	1.3822	3.0491	-2.1946	6.537	-4.7379	3.3779	-0.4003	0.4688	0.6778	0.708	1.1567	0.0363	-0.2008	-0.4383	-0.5428	1.0115	-0.019	-0.3018	0.6733	0.0836	0.8249	67.5165	39.9143	14.7493
34	6.6653	1.4035	2.2476	5.5559	0.3178	7.1077	0.3748	-0.3079	1.1718	0.8689	0.2012	0.3717	-0.9848	-0.2747	-0.241	0.5422	0.0562	0.1304	0.2529	-0.0708	0.4438	64.8193	54.0001	4.5688

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 184 through 215 )	A	184 - 215
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 216 through 255 )	A	216 - 255
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 256 through 269 )	A	256 - 269
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 270 through 303 )	A	270 - 303
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 304 through 319 )	A	304 - 319
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 320 through 354 )	A	320 - 354
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 355 through 381 )	A	355 - 381
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 382 through 393 )	A	382 - 393
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 394 through 412 )	A	394 - 412
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 184 through 196 )	B	184 - 196
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 197 through 215 )	B	197 - 215
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 216 through 281 )	B	216 - 281
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 282 through 319 )	B	282 - 319
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 320 through 354 )	B	320 - 354
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 355 through 371 )	B	355 - 371
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 372 through 412 )	B	372 - 412
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 184 through 196 )	C	184 - 196
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 197 through 215 )	C	197 - 215
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 216 through 236 )	C	216 - 236
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 237 through 255 )	C	237 - 255
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 256 through 269 )	C	256 - 269
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 270 through 303 )	C	270 - 303
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 304 through 319 )	C	304 - 319
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 320 through 342 )	C	320 - 342
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 343 through 354 )	C	343 - 354
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 355 through 381 )	C	355 - 381
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 382 through 393 )	C	382 - 393
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 394 through 412 )	C	394 - 412
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 184 through 215 )	D	184 - 215
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 216 through 255 )	D	216 - 255
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 256 through 309 )	D	256 - 309
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 310 through 361 )	D	310 - 361
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 362 through 377 )	D	362 - 377
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 378 through 412 )	D	378 - 412

-
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, 4 molecules ABCD

-
Non-polymers , 5 types, 309 molecules

-
Details

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 309 molecules

-Details

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 309 molecules

-
Details

-
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