PDB-4ph6: Structure of 3-Dehydroquinate Dehydratase from Enterococcus faecalis

ID or keywords:

Entry

Database: PDB / ID: 4ph6

Title

Structure of 3-Dehydroquinate Dehydratase from Enterococcus faecalis

Components

3-dehydroquinate dehydratase

Keywords

LYASE / (beta/alpha)8 barrel

Function / homology

Function and homology information

3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process
Similarity search - Function

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Xue, B. / Cheung, V.W. / Yew, W.S. / Robinson, R.C.

Citation

Journal: Plos One / Year: 2014
Title: Identification of Polyketide Inhibitors Targeting 3-Dehydroquinate Dehydratase in the Shikimate Pathway of Enterococcus faecalis
Authors: Cheung, V.W. / Xue, B. / Hernandez-Valladares, M. / Go, M.K. / Tung, A. / Aguda, A.H. / Robinson, R.C. / Yew, W.S.

History

Deposition	May 5, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ph6.cif.gz	205.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ph6.ent.gz	165.1 KB	Display	PDB format
PDBx/mmJSON format	4ph6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4ph6_validation.pdf.gz	435.7 KB	Display	wwPDB validaton report
Full document	4ph6_full_validation.pdf.gz	438.2 KB	Display
Data in XML	4ph6_validation.xml.gz	21.7 KB	Display
Data in CIF	4ph6_validation.cif.gz	31.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ph/4ph6 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/4ph6	HTTPS FTP

-
Related structure data

Related structure data	3j3sS S: Starting model for refinement
Similar structure data	1qfe-d 4cnp-d 3l2i-d 2yr1-d 4cno-3 1l9w-1 6h5c-d 4guj-d 4cnn-d 1dhf-d 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	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1)

Deposited unit

A: 3-dehydroquinate dehydratase

B: 3-dehydroquinate dehydratase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	42.973, 48.288, 67.429
Angle α, β, γ (deg.)	108.070, 92.860, 111.830
Int Tables number	1
Space group name H-M	P1

Details

biological unit is the same as asym.

#1: Protein	3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase Mass: 28394.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: aroD, ebsD, EF_1731 / Plasmid: pET-15b, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36923, 3-dehydroquinate dehydratase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase

Mass: 28394.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: aroD, ebsD, EF_1731 / Plasmid: pET-15b, modified / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36923, 3-dehydroquinate dehydratase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.14 Å³/Da / Density % sol: 42.41 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES sodium salt, pH 7.5, 30% (w/v) PEG 4000, 0.2 M calcium chloride

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.541 Å
Detector	Type: Bruker Platinum 135 / Detector: CCD / Date: Jun 6, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.541 Å / Relative weight: 1
Reflection	Resolution: 2.2→19.789 Å / Num. all: 21267 / Num. obs: 21267 / % possible obs: 89.23 % / Redundancy: 1.73 % / B_iso Wilson estimate: 10.966 Å² / R_merge(I) obs: 0.0594 / Net I/σ(I): 9.19
Reflection shell	Resolution: 2.2→2.3 Å / Redundancy: 1.1 % / R_merge(I) obs: 0.2072 / Mean I/σ(I) obs: 3.66 / % possible all: 46.2

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PROTEUM PLUS		data collection
SAINT		data processing
PROTEUM PLUS	3.11	data scaling
PHASER		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
PHASER		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3J3S

3j3s

Resolution: 2.2→19.789 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2548	1063	5 %	Randon selection
R_work	0.1854	20204	-	-
obs	0.1889	21267	89.23 %	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 78.94 Å² / B_iso mean: 16.0833 Å² / B_iso min: 1.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→19.789 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3746	0	0	311	4057

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3804
X-RAY DIFFRACTION	f_angle_d	1.042	5150
X-RAY DIFFRACTION	f_chiral_restr	0.04	610
X-RAY DIFFRACTION	f_plane_restr	0.004	660
X-RAY DIFFRACTION	f_dihedral_angle_d	13.862	1418

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2001-2.3001	0.2415	68	0.1815	1416	1484	49
2.3001-2.4211	0.2816	109	0.1827	1967	2076	70
2.4211-2.5725	0.2676	155	0.1838	2786	2941	99
2.5725-2.7707	0.269	157	0.1877	2798	2955	100
2.7707-3.0486	0.2692	148	0.1745	2863	3011	100
3.0486-3.4876	0.2278	143	0.1792	2811	2954	100
3.4876-4.3861	0.2305	145	0.1684	2791	2936	98
4.3861-19.7897	0.2756	138	0.2202	2772	2910	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	1.8691	0.6894	0.9891	0.4893	0.7962	1.2923	0.0132	0.1325	0.2555	-0.186	0.1255	0.0469	-0.1144	-0.0004	-0.0527	0.1528	-0.0342	-0.0239	0.1363	0.0632	0.1408	-24.4432	35.2904	-37.137
2	0.7592	0.4791	0.0707	2.1694	-0.052	0.5228	-0.0603	-0.145	0.0238	-0.1426	0.1053	-0.1106	0.0237	0.0367	-0.0119	0.1079	-0.0344	0.0998	-0.0149	0.1352	0.1367	-28.3526	26.7427	-26.8894
3	1.0908	-0.9001	-0.0484	3.4061	1.271	1.5094	-0.0155	-0.1803	-0.1955	0.0865	-0.127	0.386	0.1739	-0.0933	0.0897	0.075	-0.0236	0.0223	0.1891	0.0137	0.1378	-38.4818	18.0253	-29.744
4	1.2347	-0.1231	-0.3121	0.2613	0.2129	1.9307	-0.0732	-0.2421	-0.1158	0.1192	0.1312	0.1023	0.2658	0.0272	-0.0355	0.0938	-0.0141	0.0054	0.0841	0.0209	0.1016	-29.4187	17.8398	-28.8517
5	2.696	-1.3976	0.1684	1.4343	0.0239	0.7298	-0.0166	0.2094	-0.2315	-0.3282	0.1355	0.0504	0.1162	-0.2013	-0.0473	0.1417	-0.0533	-0.0352	0.1462	-0.0776	0.2639	-30.271	10.5863	-38.9467
6	1.0368	-0.2054	-0.3904	1.7064	-0.6042	0.8401	-0.0638	0.1486	-0.1604	-0.2409	0.093	0.0472	0.1754	-0.1791	0.0138	0.0723	-0.0244	0.0174	0.0843	-0.0086	0.0639	-30.9435	21.8755	-35.4419
7	1.1341	0.6357	-1.2543	1.387	-0.4967	1.4231	-0.1152	-0.2153	-0.4587	0.1098	-0.0077	-0.1577	0.476	0.1238	0.0516	0.3587	0.0812	0.0158	0.0846	0.1022	0.0983	-17.3145	12.2292	-23.4574
8	2.333	0.8868	0.5812	1.7589	-0.5306	0.742	-0.0458	0.1332	-0.1401	-0.1989	0.0993	-0.2146	0.0472	0.1985	-0.0121	0.4042	0.0856	0.071	0.1968	-0.0751	0.3567	-14.9976	5.681	-32.5282
9	2.0647	-1.1291	0.9274	1.2256	-1.2042	1.1948	-0.0008	0.2547	-0.4726	-0.1657	0.036	0.1957	0.3849	0.0123	-0.0603	0.1497	0.0053	0.042	0.0742	-0.0204	0.1518	-20.8791	14.0591	-40.2165
10	1.4438	0.5495	0.1858	1.5921	-0.2024	0.9219	-0.0725	0.1006	-0.3719	0.0828	0.0797	-0.3532	0.2638	0.2651	-0.0186	0.1616	0.0423	-0.0149	0.1096	-0.0313	0.1247	-11.2538	18.1797	-36.1498
11	1.4574	0.4419	1.1112	1.4182	-0.9192	2.0945	-0.1284	0.3471	-0.1351	-0.2044	0.0795	-0.0212	-0.0162	0.1416	0.0264	0.0677	0.0103	0.0365	0.1404	-0.0088	0.0856	-17.0963	23.4059	-41.6425
12	1.0547	-0.1979	-0.9517	2.8539	1.9607	2.9944	-0.1524	-0.1683	-0.3507	0.5709	0.171	-0.1501	0.4773	-0.0475	-0.055	0.1399	0.0419	-0.0441	0.1014	0.0284	0.3035	-11.3955	20.4281	-18.5001
13	2.6295	-2.9422	-0.2243	3.4221	-0.244	1.8837	-0.1135	-0.2483	0.1143	0.2047	0.0233	-0.3321	-0.0741	0.2924	0.0554	0.0757	0.0077	-0.009	0.2045	0.0497	0.0872	-3.5769	29.1888	-19.1881
14	1.2026	0.1399	0.1943	1.2021	0.4071	0.9472	-0.0758	0.3865	0.0773	-0.1643	0.0586	-0.1196	0.002	0.1772	-0.013	-0.5853	0.0089	0.0972	0.1665	-0.0304	0.1142	-5.7982	27.5208	-30.8949
15	0.949	-0.2076	0.4282	1.3654	0.1718	1.8538	-0.1574	0.0189	0.1133	0.1363	0.0465	-0.2785	-0.1718	0.0998	0.0981	0.0649	0.0155	0.0026	0.0942	0.0093	0.138	-10.7682	32.0397	-20.7501
16	2.3044	-2.0472	0.9236	2.1715	-2.3982	2.0004	-0.0577	-0.1334	-0.2036	0.198	0.104	0.0081	0.3566	-0.3346	-0.0639	0.002	0.039	-0.1422	0.0154	0.0923	-0.1774	-15.4418	31.4512	-26.7011
17	1.2117	0.5368	0.3766	3.0764	-1.2868	2.072	-0.0783	-0.043	-0.0354	0.2294	0.0535	0.4804	-0.2003	-0.253	0.0056	0.1406	0.0145	0.0181	0.1271	0.0012	0.2115	-20.1487	28.2415	-12.088
18	1.5594	0.2132	-0.1708	0.0275	-0.0208	1.4801	0.0831	-0.2594	0.1781	-0.0288	-0.0508	-0.0085	-0.1243	0.0081	-0.0218	0.1288	0.0436	0.0144	-0.0404	0.0029	0.0956	-20.4574	34.89	-21.4651
19	0.0542	-0.2052	0.1815	0.7113	-0.65	0.585	0.0223	-0.1082	-0.0416	0.1537	-0.0698	0.264	0.0359	-0.4446	0.037	0.2584	0.0109	-0.0068	0.3765	0.0119	0.1243	-31.8772	32.766	-18.6556
20	2.6879	0.1114	0.5632	1.8884	0.1121	2.5971	-0.0877	0.2159	0.3158	-0.0904	-0.0408	0.0818	-0.2584	0.041	0.1051	0.3108	-0.0051	-0.063	0.1205	0.0038	0.3368	-26.7062	43.1172	-19.0889
21	1.8068	-1.27	-0.21	1.2881	0.5211	0.9399	-0.0189	-0.1834	-0.0873	0.0718	0.1795	-0.002	0.2999	0.0128	-0.0869	0.1727	0.032	0.0296	0.1091	0.0037	0.0893	-24.2712	40.4445	12.3515
22	0.8042	-0.2966	-0.1022	1.924	0.0409	0.6898	-0.1238	-0.0391	0.0396	0.1027	0.0362	0.0296	-0.1228	-0.1598	0.05	0.0913	0.0327	-0.0433	0.106	0.0246	0.1197	-29.6501	50.9776	2.4606
23	1.3545	0.5316	0.2903	2.1538	1.107	0.5601	0.0494	0.1499	0.0213	-0.0569	-0.1205	0.1283	-0.0551	-0.0918	0.0229	0.0991	0.0432	-0.0469	0.1564	0.0107	0.1328	-38.2422	56.1254	4.9239
24	0.3633	-0.1276	-0.1139	0.1085	-0.0565	0.1632	-0.132	0.0802	0.0145	-0.1469	0.2165	-0.0244	-0.12	-0.0102	-0.0539	0.0749	-0.0248	-0.0167	0.096	-0.0147	0.0751	-30.4919	51.688	3.9682
25	2.0679	0.3934	0.4019	0.4579	-0.5375	1.0549	-0.1042	0.0773	0.2967	-0.1012	-0.0343	0.1573	-0.287	-0.1182	0.0697	0.15	-0.0234	0.0003	0.16	0.0144	0.2525	-27.6001	67.4024	4.146
26	0.3901	0.227	-0.35	0.1294	-0.1981	0.3077	0.091	0.001	0.1663	0.0122	0.0214	0.0641	-0.1961	-0.1359	-0.0473	0.2122	0.069	-0.0318	0.2545	-0.1432	0.2816	-27.3384	68.8533	13.3231
27	1.3018	0.9816	0.7672	2.926	-0.0185	1.1114	0.0728	-0.2465	-0.0069	0.4023	-0.2099	0.2002	-0.1087	-0.3797	0.0852	0.1213	0.002	0.0395	0.195	0.0144	0.1088	-34.1684	59.2782	14.187
28	0.1356	-0.2108	0.1481	0.3883	-0.0975	0.5371	-0.0692	-0.0023	-0.0063	-0.1345	-0.0004	0.044	-0.1028	0.0374	0.0444	0.1016	0.0163	0.0072	0.0396	-0.0007	0.0635	-26.2019	54.3839	7.8857
29	-0.0011	0.0254	-0.0056	1.0962	0.5741	0.5174	0.0176	0.0827	0.4704	0.126	0.0323	-0.1624	-0.2664	0.1824	0.0138	0.233	-0.0504	0.0317	0.1831	0.0006	0.2149	-16.4186	66.1533	0.7222
30	2.5625	-0.2363	-0.0863	0.9253	-0.3648	1.4429	-0.0292	-0.2402	0.4692	0.1912	0.0249	-0.0413	-0.3378	0.078	0.0431	0.1991	-0.0246	-0.0053	0.1065	-0.0238	0.1189	-19.7992	61.2684	13.9378
31	0.6841	-0.0078	-0.0743	0.6846	-0.1852	1.338	-0.1819	-0.0935	0.0694	-0.0584	-0.1372	-0.323	-0.1732	0.2084	0.1493	0.0837	-0.0556	0.0205	0.151	0.0073	0.1312	-8.9506	58.4567	11.8836
32	1.3776	-0.2161	-1.0161	0.9332	-0.3042	1.5362	-0.1276	-0.1978	0.2052	0.0441	0.0007	-0.0731	-0.0403	0.0492	0.085	0.0742	-0.0255	-0.0077	0.1146	-0.0104	0.0955	-16.0971	52.8447	12.774
33	2.1941	-1.7209	-0.8809	1.7159	1.3963	1.7212	-0.0784	0.0836	0.4088	-0.1547	-0.0558	-0.1737	-0.3881	0.0978	0.1153	0.2926	-0.0928	-0.0135	0.2267	-0.001	0.2037	-11.0088	56.3545	-9.6858
34	2.3827	1.5124	0.4668	1.537	-0.6984	1.7915	-0.0527	0.0561	-0.0159	-0.1664	-0.1083	-0.2954	0.1953	0.156	0.0645	0.1122	0.0261	-0.0042	0.1414	-0.1057	0.1101	-3.3628	47.0786	-6.3813
35	0.6864	-0.0432	-0.3193	0.511	0.0293	0.8196	-0.1553	-0.204	0.2057	0.0013	-0.0735	-0.1002	-0.1954	0.2424	0.1481	0.0283	0.0155	-0.0226	0.1189	-0.0124	0.1068	-9.022	48.5581	3.8211
36	1.4074	-0.3086	0.7795	1.2372	0.0437	1.6149	-0.0462	0.1757	-0.0302	-0.175	-0.0983	-0.1988	0.2042	0.3582	0.1435	0.0582	0.0042	0.0315	0.1169	-0.0072	0.1232	-10.172	41.7668	-4.5103
37	1.1638	-1.4155	1.0322	2.0894	-1.4371	1.003	-0.0935	-0.0326	0.1011	-0.0741	-0.0375	0.2846	-0.1746	-0.4912	0.0675	0.2861	0.0275	-0.0501	0.0964	-0.1022	0.1319	-18.6355	48.4098	-10.3148
38	2.1493	1.3318	-1.4478	7.6618	0.613	2.9956	-0.037	0.5357	0.0647	-0.3585	-0.0529	0.2569	-0.0412	-0.1426	0.0447	0.1038	-0.0163	-0.0195	0.1923	-0.0046	0.078	-21.7627	42.714	-9.0068
39	0.9436	-0.2327	-0.4325	0.9696	0.573	2.0195	0.2194	0.2502	-0.1568	-0.3138	0.0613	0.225	-0.0907	-0.5635	-0.0529	0.2153	0.0047	0.0472	0.1165	-0.0001	0.0439	-25.1411	42.4619	-3.6165
40	0.8336	-0.3284	-0.4494	0.8593	0.7039	0.615	-0.0695	-0.0394	-0.3185	0.0208	-0.0768	0.0519	0.3224	0.0398	0.091	0.189	-0.0084	0.0256	0.2168	0.0972	0.1794	-28.461	34.897	-5.6284

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 3:12)	A	3 - 12
2	X-RAY DIFFRACTION	2	(chain A and resid 13:26)	A	13 - 26
3	X-RAY DIFFRACTION	3	(chain A and resid 27:38)	A	27 - 38
4	X-RAY DIFFRACTION	4	(chain A and resid 39:56)	A	39 - 56
5	X-RAY DIFFRACTION	5	(chain A and resid 57:67)	A	57 - 67
6	X-RAY DIFFRACTION	6	(chain A and resid 68:81)	A	68 - 81
7	X-RAY DIFFRACTION	7	(chain A and resid 82:90)	A	82 - 90
8	X-RAY DIFFRACTION	8	(chain A and resid 91:96)	A	91 - 96
9	X-RAY DIFFRACTION	9	(chain A and resid 97:111)	A	97 - 111
10	X-RAY DIFFRACTION	10	(chain A and resid 112:129)	A	112 - 129
11	X-RAY DIFFRACTION	11	(chain A and resid 130:140)	A	130 - 140
12	X-RAY DIFFRACTION	12	(chain A and resid 141:149)	A	141 - 149
13	X-RAY DIFFRACTION	13	(chain A and resid 150:154)	A	150 - 154
14	X-RAY DIFFRACTION	14	(chain A and resid 155:165)	A	155 - 165
15	X-RAY DIFFRACTION	15	(chain A and resid 166:197)	A	166 - 197
16	X-RAY DIFFRACTION	16	(chain A and resid 198:203)	A	198 - 203
17	X-RAY DIFFRACTION	17	(chain A and resid 204:211)	A	204 - 211
18	X-RAY DIFFRACTION	18	(chain A and resid 212:225)	A	212 - 225
19	X-RAY DIFFRACTION	19	(chain A and resid 226:245)	A	226 - 245
20	X-RAY DIFFRACTION	20	(chain A and resid 246:251)	A	246 - 251
21	X-RAY DIFFRACTION	21	(chain B and resid 3:12)	B	3 - 12
22	X-RAY DIFFRACTION	22	(chain B and resid 13:28)	B	13 - 28
23	X-RAY DIFFRACTION	23	(chain B and resid 29:38)	B	29 - 38
24	X-RAY DIFFRACTION	24	(chain B and resid 39:49)	B	39 - 49
25	X-RAY DIFFRACTION	25	(chain B and resid 50:56)	B	50 - 56
26	X-RAY DIFFRACTION	26	(chain B and resid 57:61)	B	57 - 61
27	X-RAY DIFFRACTION	27	(chain B and resid 62:71)	B	62 - 71
28	X-RAY DIFFRACTION	28	(chain B and resid 72:83)	B	72 - 83
29	X-RAY DIFFRACTION	29	(chain B and resid 84:94)	B	84 - 94
30	X-RAY DIFFRACTION	30	(chain B and resid 95:115)	B	95 - 115
31	X-RAY DIFFRACTION	31	(chain B and resid 116:129)	B	116 - 129
32	X-RAY DIFFRACTION	32	(chain B and resid 130:143)	B	130 - 143
33	X-RAY DIFFRACTION	33	(chain B and resid 144:148)	B	144 - 148
34	X-RAY DIFFRACTION	34	(chain B and resid 149:153)	B	149 - 153
35	X-RAY DIFFRACTION	35	(chain B and resid 154:174)	B	154 - 174
36	X-RAY DIFFRACTION	36	(chain B and resid 175:201)	B	175 - 201
37	X-RAY DIFFRACTION	37	(chain B and resid 202:209)	B	202 - 209
38	X-RAY DIFFRACTION	38	(chain B and resid 210:215)	B	210 - 215
39	X-RAY DIFFRACTION	39	(chain B and resid 216:242)	B	216 - 242
40	X-RAY DIFFRACTION	40	(chain B and resid 243:251)	B	243 - 251

-
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

-
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