PDB-5f4z: The crystal structure of an epoxide hydrolase from Streptomyces c...

ID or keywords:

Entry

Database: PDB / ID: 5f4z

Title

The crystal structure of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus

Components

Epoxide hydrolase

Keywords

HYDROLASE / epoxide hydrolase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro

Function / homology

Function and homology information

cis-stilbene-oxide hydrolase activity
Similarity search - Function

Biological species

Streptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.82 Å

Authors

Tan, K. / Li, H. / Jedrzejczak, R. / BABNIGG, G. / BINGMAN, C.A. / YENNAMALLI, R. / LOHMAN, J. / Chang, C.Y. / Shen, B. / Phillips Jr., G.N. ...

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus
Authors: Tan, K. / Li, H. / Jedrzejczak, R. / BABNIGG, G. / BINGMAN, C.A. / YENNAMALLI, R. / LOHMAN, J. / Chang, C.Y. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A.

History

Deposition	Dec 3, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 17, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Feb 6, 2019	Group: Data collection / Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 23, 2020	Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5f4z.cif.gz	777.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5f4z.ent.gz	669.7 KB	Display	PDB format
PDBx/mmJSON format	5f4z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5f4z_validation.pdf.gz	538.4 KB	Display	wwPDB validaton report
Full document	5f4z_full_validation.pdf.gz	565.1 KB	Display
Data in XML	5f4z_validation.xml.gz	81.5 KB	Display
Data in CIF	5f4z_validation.cif.gz	116.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/5f4z ftp://data.pdbj.org/pub/pdb/validation_reports/f4/5f4z	HTTPS FTP

-
Related structure data

Similar structure data	4qa9-1 3g02-d 3g0i-d 5veb-1 3ruc-2 2qnr-d 6i1f-d 4xza-d 2ouy-d 6njk-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC109148 TargetTrack: NatPro-GO.119842

Similar structure data

Other databases

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Epoxide hydrolase

B: Epoxide hydrolase

C: Epoxide hydrolase

D: Epoxide hydrolase

E: Epoxide hydrolase

hetero molecules

221 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Epoxide hydrolase

B: Epoxide hydrolase

hetero molecules

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

2

C: Epoxide hydrolase

D: Epoxide hydrolase

hetero molecules

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

3

E: Epoxide hydrolase

hetero molecules

E: Epoxide hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	179.356, 93.068, 134.059
Angle α, β, γ (deg.)	90.00, 115.33, 90.00
Int Tables number	5
Space group name H-M	C121

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein	Epoxide hydrolase Mass: 43775.891 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces carzinostaticus subsp. neocarzinostaticus (bacteria) Plasmid: pMCSG81 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84HB1

-
Non-polymers , 7 types, 1209 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-5V4 / (1~{R},2~{R})-2,3-dihydro-1~{H}-indene-1,2-diol Mass: 150.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₉H₁₀O₂
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1192 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.16 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.16M MgCl2, 0.08M Tris:HCl, 24% (w/v) PEG 4000, 20% (v/v) Glycerol

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 1.82→34 Å / Num. obs: 177945 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / R_merge(I) obs: 0.062 / Net I/σ(I): 31
Reflection shell	Resolution: 1.82→1.85 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.661 / Mean I/σ(I) obs: 1.32 / % possible all: 99.1

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Resolution: 1.82→33.267 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2004	8896	5.01 %	Random selection
R_work	0.1599	-	-	-
obs	0.1619	177658	99.67 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.82→33.267 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15144	0	133	1192	16469

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15988
X-RAY DIFFRACTION	f_angle_d	1.082	21933
X-RAY DIFFRACTION	f_dihedral_angle_d	12.422	5724
X-RAY DIFFRACTION	f_chiral_restr	0.045	2327
X-RAY DIFFRACTION	f_plane_restr	0.006	2881

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 (%)
1.82-1.8407	0.3367	290	0.2869	5528	X-RAY DIFFRACTION	98
1.8407-1.8623	0.3048	285	0.2612	5618	X-RAY DIFFRACTION	99
1.8623-1.885	0.2827	283	0.2471	5592	X-RAY DIFFRACTION	100
1.885-1.9089	0.2986	292	0.2306	5638	X-RAY DIFFRACTION	100
1.9089-1.934	0.2647	292	0.2337	5580	X-RAY DIFFRACTION	100
1.934-1.9605	0.2691	298	0.2171	5593	X-RAY DIFFRACTION	100
1.9605-1.9885	0.2344	270	0.2011	5631	X-RAY DIFFRACTION	100
1.9885-2.0182	0.2349	294	0.1894	5700	X-RAY DIFFRACTION	100
2.0182-2.0497	0.2318	273	0.1856	5588	X-RAY DIFFRACTION	100
2.0497-2.0833	0.2213	293	0.1849	5609	X-RAY DIFFRACTION	100
2.0833-2.1192	0.2162	304	0.1809	5642	X-RAY DIFFRACTION	100
2.1192-2.1578	0.2424	275	0.1726	5647	X-RAY DIFFRACTION	100
2.1578-2.1993	0.2076	320	0.1625	5633	X-RAY DIFFRACTION	100
2.1993-2.2442	0.2143	314	0.1629	5584	X-RAY DIFFRACTION	100
2.2442-2.2929	0.198	298	0.1676	5604	X-RAY DIFFRACTION	100
2.2929-2.3463	0.2245	328	0.1646	5636	X-RAY DIFFRACTION	100
2.3463-2.4049	0.2074	303	0.1576	5615	X-RAY DIFFRACTION	100
2.4049-2.4699	0.2014	310	0.1537	5603	X-RAY DIFFRACTION	100
2.4699-2.5426	0.2123	321	0.164	5586	X-RAY DIFFRACTION	100
2.5426-2.6246	0.2168	334	0.1654	5628	X-RAY DIFFRACTION	100
2.6246-2.7184	0.2106	284	0.1555	5656	X-RAY DIFFRACTION	100
2.7184-2.8272	0.2189	318	0.1636	5601	X-RAY DIFFRACTION	100
2.8272-2.9558	0.206	273	0.1657	5680	X-RAY DIFFRACTION	100
2.9558-3.1115	0.2142	274	0.1625	5659	X-RAY DIFFRACTION	100
3.1115-3.3063	0.2034	309	0.1583	5635	X-RAY DIFFRACTION	100
3.3063-3.5613	0.1828	284	0.1521	5641	X-RAY DIFFRACTION	99
3.5613-3.9192	0.1714	281	0.1389	5662	X-RAY DIFFRACTION	99
3.9192-4.4851	0.1553	306	0.1249	5635	X-RAY DIFFRACTION	99
4.4851-5.6463	0.1732	280	0.1292	5662	X-RAY DIFFRACTION	99
5.6463-33.2728	0.1494	310	0.1423	5676	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	1.4449	-1.0011	0.2484	2.1788	-1.2653	2.1553	-0.0679	-0.0495	-0.2644	0.1845	0.08	0.2575	0.0048	-0.0354	-0.0367	0.1565	-0.0373	0.0218	0.117	-0.0305	0.2356	-6.197	4.5968	28.6691
2	2.9901	-0.8829	0.6417	1.839	-0.759	0.9356	-0.0239	-0.186	-0.4367	0.0951	0.0533	0.3108	0.169	-0.1323	-0.0644	0.1966	-0.0053	0.0677	0.1272	-0.02	0.1724	1.0439	-3.6983	29.4481
3	0.9571	-0.1066	-0.1553	0.8077	0.2013	1.3381	-0.0396	0.0228	-0.1144	0.0644	-0.0148	-0.106	0.125	0.1054	0.0367	0.1488	0.0218	-0.0035	0.1534	0.0121	0.1962	20.0872	-2.9989	21.8728
4	1.1695	-0.5133	-0.4877	0.7571	0.3728	1.2128	0.0069	0.1413	-0.0395	-0.0202	-0.0291	0.0791	0.0314	-0.0921	0.0257	0.1249	0.0052	-0.0139	0.1473	-0.0013	0.1622	4.035	8.5102	19.3211
5	2.6075	-2.1945	-2.118	2.0406	1.9619	2.6144	0.1089	-0.1062	0.3363	-0.2055	0.0585	-0.416	-0.3726	0.153	-0.179	0.1923	-0.0063	-0.0096	0.1742	0.054	0.2195	20.6299	9.0217	12.5171
6	4.0397	-0.5325	-1.7761	2.1921	-0.8478	3.0069	0.0345	0.2604	-0.0406	-0.1178	-0.0838	-0.0415	0.0528	-0.0056	-0.001	0.1478	0.0063	-0.0224	0.1328	-0.0346	0.107	18.9992	-0.7146	6.7741
7	8.9611	-1.1344	-2.6311	4.7447	-0.7566	4.8241	-0.069	0.0215	-0.3513	-0.1588	-0.0855	-0.1269	0.3733	0.3642	0.2705	0.2273	0.0294	0.0147	0.1471	-0.0199	0.1818	22.2797	-12.2907	11.2361
8	3.2635	-1.045	0.0361	2.5222	-0.5142	0.8554	-0.0388	-0.0468	-0.2305	0.1566	0.1005	0.2983	0.0025	-0.1146	-0.049	0.1756	0.0059	0.0279	0.1327	-0.0291	0.089	-9.5799	22.1114	34.5109
9	2.7927	-1.6826	0.9117	2.143	-1.1536	3.0245	-0.0515	-0.2568	0.0106	0.1988	0.1536	0.2554	-0.1094	-0.3932	-0.0775	0.1405	-0.0243	0.0272	0.1096	-0.0127	0.2008	-15.1022	31.1588	31.8511
10	0.8952	0.0512	-0.1052	2.2507	0.2641	1.4644	0.0507	0.1219	0.1308	-0.1289	-0.0235	0.1429	-0.2615	-0.1128	-0.0121	0.1853	0.0695	-0.0105	0.1949	0.0292	0.1833	-12.9209	43.1552	18.1317
11	3.3478	0.6558	0.2982	1.3869	-0.0466	1.1472	0.0042	0.8062	-0.0261	-0.3695	0.0254	-0.2265	-0.2754	0.2511	-0.0311	0.2903	0.0154	0.087	0.3611	0.0358	0.2318	5.6762	44.8337	10.8096
12	4.4567	6.1251	0.5343	8.4653	0.7488	0.0308	0.0581	0.0003	-0.0783	-0.0097	-0.0081	-0.3317	-0.0949	0.0568	-0.1046	0.1847	-0.0056	0.0233	0.1991	-0.0009	0.2212	10.1532	31.3858	19.2715
13	1.1475	0.1028	-0.0623	1.1325	0.5123	1.1072	0.0223	-0.068	-0.0146	0.0834	-0.0083	0.0579	-0.0296	-0.0418	-0.0083	0.1815	0.0227	-0.0049	0.1707	0.0077	0.1855	-4.6382	26.9906	28.7041
14	1.3745	1.0387	0.4334	4.0624	-0.7069	0.7142	0.0459	0.3618	0.0867	-0.5745	-0.0023	-0.3481	-0.0956	0.015	-0.0691	0.223	0.0538	0.0704	0.2784	0.047	0.2171	4.7884	39.5148	12.5361
15	4.5352	-0.6969	-1.5998	3.8946	-1.3488	3.8474	0.1121	0.2656	0.4696	-0.0212	-0.1097	-0.2597	-0.3969	0.1975	-0.0182	0.1958	-0.0273	-0.0211	0.1746	0.0314	0.2503	5.0314	48.221	19.7189
16	2.2256	-0.3156	0.8305	3.1943	-1.3127	3.4833	0.1432	0.2999	0.7026	-0.2034	-0.0738	-0.2001	-0.7229	0.2169	-0.051	0.4018	0.0475	0.0546	0.1884	0.0871	0.4467	-4.9244	57.5355	20.0638
17	0.5345	-0.139	-1.162	1.214	-0.1836	3.0746	0.0582	-0.0131	0.0869	-0.0425	-0.0569	-0.1201	-0.1678	0.0598	-0.0022	0.0765	-0.0352	-0.0052	0.1779	-0.0206	0.2157	57.9726	43.1857	15.9175
18	1.7048	1.0592	0.6808	1.598	1.494	3.801	-0.0669	0.1035	0.0578	-0.1054	0.1176	-0.1231	-0.1112	0.3257	-0.0635	0.1397	-0.0039	0.0154	0.1389	0.0162	0.207	58.9268	35.9778	8.7115
19	1.9693	-0.1884	-0.8989	2.6191	0.1526	2.5815	-0.0878	0.1031	-0.0803	-0.1505	-0.0329	-0.1277	0.4353	0.0526	0.0956	0.2078	-0.0204	0.0164	0.1884	-0.0158	0.1436	51.6144	21.1079	4.4758
20	1.3351	-0.1608	0.3115	1.8916	-0.261	3.2661	-0.0902	0.0205	-0.2458	0.0173	0.139	0.1225	0.4314	-0.3837	-0.0225	0.2479	-0.0832	0.0295	0.2375	-0.0233	0.2545	43.6326	13.3431	15.9943
21	1.2253	-1.8194	0.4774	3.4763	-0.5624	1.4877	-0.0415	-0.1727	0.017	0.2003	0.1089	-0.0196	0.1469	-0.0622	-0.0449	0.2185	-0.0569	0.0126	0.2707	-0.0257	0.2593	45.5969	24.3503	30.7489
22	0.3733	-0.3368	-0.3616	2.2571	-0.4873	1.1183	-0.0164	-0.0079	0.0406	0.064	-0.0224	-0.139	-0.04	0.1175	0.0384	0.1599	-0.034	0.0008	0.2253	-0.0362	0.2084	53.8441	35.7326	19.2452
23	0.2957	0.1166	0.4757	4.3938	-0.0972	1.4009	0.0076	-0.0899	0.0247	0.2271	-0.0247	0.3621	0.2567	-0.3338	0.072	0.2562	-0.0873	0.0521	0.2968	-0.0222	0.2201	42.5317	16.7172	22.6639
24	4.1453	1.9915	-0.2915	3.5691	0.547	2.4641	0.0357	-0.0448	-0.4576	-0.1049	-0.0491	-0.3126	0.6021	0.0414	0.0122	0.3345	0.032	-0.0105	0.1817	0.0232	0.2335	54.2602	9.5537	17.5459
25	1.3484	0.2679	-0.1651	2.3049	0.7252	2.4279	0.0962	0.0285	0.2253	0.1	0.0252	0.024	-0.4226	0.033	-0.0635	0.2441	0.005	0.0505	0.1438	0.0058	0.2496	43.6248	59.3022	24.1425
26	1.5704	-0.4225	-0.3979	1.7108	0.1653	1.5445	0.1344	-0.2693	0.2295	0.3707	-0.0464	0.1074	-0.517	0.0104	-0.0914	0.4877	-0.0625	0.0672	0.281	-0.096	0.2472	39.5363	57.1458	49.4939
27	4.0663	2.3402	1.6727	3.2593	2.0579	2.9089	0.2199	-0.2765	-0.5254	0.3545	0.0279	-0.1247	-0.0497	-0.2739	-0.2447	0.2681	0.0318	0.0316	0.237	0.0776	0.299	26.1879	38.0803	44.589
28	1.4534	0.1268	-0.3982	0.6276	-0.1273	1.0151	0.0648	-0.1092	0.0554	0.1612	-0.0025	0.0616	-0.1428	-0.0001	-0.0424	0.2467	-0.025	0.0214	0.2293	-0.045	0.2346	40.6509	46.5067	33.0402
29	2.1043	0.3591	0.1815	2.6554	1.1818	2.211	0.1798	-0.2983	0.1309	0.4008	0.0078	0.2212	-0.3874	-0.4463	-0.1744	0.3771	0.0567	0.1139	0.2899	-0.0022	0.2642	22.9659	49.907	48.5298
30	1.4259	0.5405	-0.3495	1.5103	0.1656	0.5527	-0.1822	-0.035	-0.3341	-0.1642	-0.0167	-0.4194	0.1746	0.0907	0.1808	0.3506	0.0644	0.0944	0.2048	0.074	0.2954	81.2867	7.529	52.7903
31	3.6661	-0.9636	2.3371	4.2634	-2.3554	3.8723	-0.2717	-0.2334	0.1651	0.0238	0.2065	-0.1177	-0.3763	-0.1331	0.0218	0.2454	0.0192	0.0286	0.1482	0.0108	0.167	84.1055	29.1823	53.3608
32	1.1351	0.0651	-0.371	1.5995	0.1552	0.5533	-0.0681	0.0408	-0.0796	-0.1483	-0.0909	-0.0369	0.1038	0.0131	0.155	0.2659	0.0193	0.024	0.1653	0.012	0.1494	68.2505	14.5792	52.8684
33	4.5001	1.9222	-1.6069	2.4953	-1.6649	1.2184	0.2993	-0.4918	0.3952	0.1396	-0.0906	0.0088	-0.3513	0.1131	-0.2144	0.2791	0.027	0.0073	0.1599	-0.0185	0.221	76.9295	30.492	53.9703
34	1.999	0.741	-0.2638	4.4232	-0.0043	0.5893	-0.1003	0.0594	-0.0385	-0.3613	-0.0035	-0.3619	0.0886	0.0543	0.0911	0.3327	0.02	0.0931	0.176	0.0542	0.1913	85.1426	27.2968	42.1365

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 80 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 81 through 215 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 216 through 306 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 307 through 341 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 342 through 369 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 370 through 388 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 39 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 80 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 81 through 187 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 188 through 215 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 216 through 242 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 243 through 306 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 307 through 341 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 342 through 369 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 370 through 390 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1 through 39 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 40 through 80 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 81 through 164 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 165 through 215 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 216 through 242 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 243 through 306 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 307 through 341 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 342 through 387 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 1 through 65 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 66 through 187 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 188 through 231 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 232 through 325 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 326 through 391 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 1 through 164 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 165 through 215 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 216 through 306 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 307 through 341 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 342 through 388 )

-
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, 5 molecules ABCDE

-
Non-polymers , 7 types, 1209 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, 5 molecules ABCDE

-Non-polymers , 7 types, 1209 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, 5 molecules ABCDE

-
Non-polymers , 7 types, 1209 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