PDB-5idu: Crystal structure of an acyl-CoA dehydrogenase domain protein fro...

ID or keywords:

Entry

Database: PDB / ID: 5idu

Title

Crystal structure of an acyl-CoA dehydrogenase domain protein from Burkholderia phymatum bound to FAD

Components

Acyl-CoA dehydrogenase domain protein

Keywords

OXIDOREDUCTASE / NIAID / structural genomics / FAD / tetramer / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Burkholderia phymatum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Edwards, T.E.

Citation

Journal: To Be Published
Title: Crystal structure of an acyl-CoA dehydrogenase domain protein from Burkholderia phymatum bound to FAD
Authors: Edwards, T.E. / Mayclin, S.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Feb 24, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2016	Group: Data collection
Revision 1.2	Sep 27, 2023	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 / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5idu.cif.gz	627 KB	Display	PDBx/mmCIF format
PDB format	pdb5idu.ent.gz	515.2 KB	Display	PDB format
PDBx/mmJSON format	5idu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/id/5idu ftp://data.pdbj.org/pub/pdb/validation_reports/id/5idu	HTTPS FTP

-
Related structure data

Related structure data	4l1fS S: Starting model for refinement
Similar structure data	5jsc-1 4l1f-1 4x28-d 2eba-2 3mpi-2 3mpi-1 1ege-d 2eba-1 2vig-2 4p13-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
Other databases	TargetTrack: BuphA.00027.f

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Acyl-CoA dehydrogenase domain protein

B: Acyl-CoA dehydrogenase domain protein

C: Acyl-CoA dehydrogenase domain protein

D: Acyl-CoA dehydrogenase domain protein

hetero molecules

181 kDa, 4 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)	84.180, 108.420, 189.440
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Acyl-CoA dehydrogenase domain protein Mass: 44303.180 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia phymatum (bacteria) / Strain: DSM 17167 / STM815 / Gene: Bphy_4072 / Production host: Escherichia coli (E. coli) / References: UniProt: B2JPK4
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1189 / 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: 2.44 Å³/Da / Density % sol: 49.57 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: BuphA.00027.f.B1.PS02558 at 21.1 mg/mL against Morepheus D6 10% PEG 8000, 20% ethylene glycol, 0.02 M each alcohol, 0.1 M MOPS/Hepes pH 7.5, crystal tracking ID 269543d6, unique puck ID evl4-1

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 126600 / % possible obs: 99.9 % / Redundancy: 5 % / CC_1/2: 0.997 / R_merge(I) obs: 0.09 / Net I/σ(I): 10.1
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 5 % / R_merge(I) obs: 0.501 / Mean I/σ(I) obs: 3.33 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_2313: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L1F

4l1f

Resolution: 1.95→47.36 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 17.73

	R_factor	Num. reflection	% reflection
R_free	0.1896	2007	1.59 %
R_work	0.1537	-	-
obs	0.1543	126592	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→47.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11806	0	256	1189	13251

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	12422
X-RAY DIFFRACTION	f_angle_d	0.783	16892
X-RAY DIFFRACTION	f_dihedral_angle_d	14.251	7230
X-RAY DIFFRACTION	f_chiral_restr	0.048	1873
X-RAY DIFFRACTION	f_plane_restr	0.005	2185

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 (%)
1.9501-1.9988	0.2637	129	0.2053	8828	X-RAY DIFFRACTION	100
1.9988-2.0529	0.2633	164	0.2012	8776	X-RAY DIFFRACTION	100
2.0529-2.1133	0.2534	143	0.1859	8811	X-RAY DIFFRACTION	100
2.1133-2.1815	0.1898	145	0.1696	8803	X-RAY DIFFRACTION	100
2.1815-2.2595	0.2038	142	0.1624	8804	X-RAY DIFFRACTION	100
2.2595-2.3499	0.2105	116	0.1521	8866	X-RAY DIFFRACTION	100
2.3499-2.4569	0.1884	160	0.1515	8848	X-RAY DIFFRACTION	100
2.4569-2.5864	0.1955	132	0.1516	8871	X-RAY DIFFRACTION	100
2.5864-2.7484	0.1899	146	0.1546	8851	X-RAY DIFFRACTION	100
2.7484-2.9606	0.1818	135	0.1515	8907	X-RAY DIFFRACTION	100
2.9606-3.2585	0.1817	140	0.1564	8912	X-RAY DIFFRACTION	100
3.2585-3.7298	0.1762	139	0.1492	8971	X-RAY DIFFRACTION	100
3.7298-4.6985	0.1546	172	0.1261	9011	X-RAY DIFFRACTION	100
4.6985-47.3739	0.1826	144	0.1485	9326	X-RAY DIFFRACTION	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	1.2985	-0.5895	-0.3991	2.12	0.9633	1.7508	-0.116	0.1597	-0.0894	-0.0114	0.1566	-0.4089	0.0382	0.2258	-0.0489	0.0959	-0.0008	-0.0089	0.2243	-0.0469	0.2335	45.4687	-23.1081	-24.7914
2	3.5929	1.5659	1.508	2.4342	2.3192	2.2228	-0.033	0.6821	-0.0636	-0.5545	0.2106	-0.1825	-0.3053	0.3264	-0.0991	0.1909	-0.0167	0.0531	0.3847	-0.0978	0.227	38.532	-35.9896	-43.4612
3	0.9419	0.1506	-0.1433	1.7514	0.4929	0.1827	0.0153	-0.0128	-0.1754	0.1322	0.1299	-0.2595	0.0482	0.0903	-0.1237	0.1034	0.0237	-0.0365	0.1192	-0.0426	0.1845	37.996	-36.2978	-26.9869
4	0.984	0.3067	0.2463	1.0093	-0.2743	1.1568	0.1372	-0.0421	-0.3457	-0.0087	0.0432	-0.1143	0.1365	0.079	-0.1203	0.1548	0.0373	-0.0654	0.0798	-0.0432	0.2005	28.3819	-47.2163	-28.6116
5	1.0878	0.0343	-0.1163	2.0789	-0.2572	1.1512	0.0688	-0.1185	-0.1883	0.1073	0.1213	0.1172	0.2546	-0.0101	-0.1517	0.1576	0.0098	-0.0752	0.0961	0.0042	0.1595	19.0697	-51.569	-29.5267
6	0.5476	0.1654	0.2851	1.0867	0.0469	0.2418	0.0405	0.0487	-0.1439	-0.0172	0.0652	-0.066	0.0916	0.0441	-0.0861	0.1139	0.0206	-0.0158	0.0968	-0.0224	0.1199	25.9255	-39.2908	-32.1926
7	0.8696	-0.0668	0.102	0.5476	-0.1951	1.2986	-0.034	0.0561	0.0326	-0.0455	0.0586	-0.0746	0.0233	0.0049	-0.0713	0.0965	-0.0152	-0.0252	0.0929	-0.029	0.1124	31.7987	-12.3843	-27.5827
8	0.6949	-0.0188	0.3394	0.6563	-0.7875	2.2509	0.0501	0.0982	-0.0483	-0.0773	-0.0028	-0.0204	0.1627	0.1936	-0.0253	0.1056	0.0071	-0.0127	0.1039	-0.0214	0.1238	25.4472	-20.4495	-34.8861
9	2.4037	-0.0029	-0.1809	2.7242	0.7518	6.3183	-0.0245	-0.3805	-0.2838	0.3456	0.0495	0.0173	0.3044	-0.098	-0.0487	0.1592	-0.007	-0.0333	0.1692	0.0674	0.2027	15.9687	-25.7352	-11.1542
10	2.159	-0.9666	-0.8673	1.2142	0.9795	3.1878	-0.0401	0.1822	-0.0733	-0.0636	-0.0777	0.1099	0.0513	-0.2983	0.1483	0.0926	-0.0301	-0.0185	0.0789	0.0143	0.1426	-7.0165	-12.2764	-51.2071
11	7.615	0.3001	-2.0867	2.4506	1.2781	1.362	-0.1	0.2364	-0.9952	-0.1574	0.1012	-0.1581	0.4818	0.2265	-0.018	0.2683	0.0106	-0.0043	0.1978	-0.044	0.25	10.31	-22.5245	-63.1946
12	1.0188	0.4884	-0.8148	0.3533	-0.0068	1.9373	0.0323	0.3512	0.1924	-0.036	-0.0755	0.0248	-0.0782	-0.1403	0.014	0.1244	0.0081	-0.015	0.1821	0.0419	0.1191	0.9859	-7.4304	-59.6653
13	0.7655	0.04	-0.2384	1.0817	-0.4933	1.1196	0.0381	0.3133	0.167	-0.0725	-0.095	-0.1262	-0.0659	0.1909	0.0523	0.1495	0.0104	0.0106	0.2438	0.0756	0.1432	20.5263	-3.6357	-65.5873
14	0.8455	-0.04	-0.2529	0.9323	-0.104	1.4275	0.0295	0.3336	0.2886	-0.4199	-0.1135	-0.2474	-0.0365	0.2271	0.0682	0.1961	0.0008	0.0338	0.3188	0.1262	0.2636	24.9496	1.2874	-70.9195
15	1.297	0.8385	-0.759	2.26	-1.7874	2.0922	0.0049	0.0785	0.1133	-0.0865	0.0716	0.0654	-0.0691	-0.0406	-0.0979	0.1131	0.0043	-0.0094	0.099	0.0019	0.0932	8.2887	-10.4963	-48.0256
16	0.5651	-0.4822	0.3091	1.6567	-0.5376	0.5843	-0.0243	-0.0427	-0.064	-0.0365	0.0341	-0.0158	0.0853	-0.0239	0.0227	0.0873	0.0044	0.0046	0.0875	0.005	0.1203	2.5625	-15.5306	-35.3535
17	0.7217	-0.6662	0.237	1.6447	-0.2171	0.3169	0.0305	0.15	0.0743	-0.1862	-0.05	-0.0828	0.0125	0.0617	0.0258	0.1056	-0.0007	-0.0004	0.1335	0.0192	0.1075	12.7832	-14.1791	-42.8539
18	2.7692	-0.5542	-0.7026	5.5732	1.8556	3.8858	-0.0863	0.2679	0.2763	-0.3243	0.1209	0.1186	-0.3314	-0.0406	-0.0083	0.1738	-0.0411	-0.0165	0.2135	0.0879	0.1697	15.0442	8.5934	-40.1076
19	1.5738	-1.0222	1.4578	1.5618	-1.8608	2.8888	-0.0885	0.0277	0.1172	0.0496	0.1147	0.0637	-0.2635	-0.012	-0.0563	0.1886	0.0055	-0.0198	0.1197	-0.0041	0.1534	-8.2883	9.9106	-45.0953
20	1.4329	0.0737	-1.0303	1.5159	0.5114	6.5731	0.2028	-0.3903	0.4242	0.2759	0.0032	-0.1072	-0.8521	0.3972	-0.1815	0.3484	-0.0229	0.0584	0.1721	-0.0239	0.2644	-10.0915	15.1919	-19.0872
21	1.4259	-0.4137	-1.3092	0.8115	-0.341	2.0337	0.0453	-0.2014	-0.0671	0.1005	0.0818	0.1134	-0.3064	-0.0993	-0.1139	0.1667	0.0322	0.0351	0.1534	0.0382	0.1476	-15.4183	5.2674	-21.8839
22	0.7684	0.224	-0.0774	0.5571	0.0751	1.2824	-0.0437	-1.237	-0.5082	0.2763	0.046	0.0131	-0.0451	-0.062	-0.0084	0.2466	0.0079	0.0581	0.6172	0.3139	0.3071	-17.8345	-5.4475	-4.6725
23	2.0652	-0.1826	0.4906	0.1556	-0.2917	1.0373	-0.1048	-0.0538	-0.5553	-0.3524	0.0664	-0.0187	0.163	-0.2914	-0.0426	0.2507	0.0567	0.1272	0.2377	0.1249	0.4199	-19.0937	-10.9624	-16.207
24	1.4937	-0.0682	0.3896	0.5871	-0.0182	0.6825	-0.0152	-0.1444	0.1167	0.0462	-0.0002	-0.0234	-0.1128	0.0206	0.0081	0.1239	0.0081	0.0028	0.1058	0.0202	0.1012	6.3092	3.2038	-28.5448
25	2.5375	2.0161	0.8721	3.9166	0.6214	1.0727	0.1245	-0.7415	-0.0058	0.0827	-0.2407	0.3466	-0.0395	-0.1878	0.1228	0.2862	0.0051	0.0064	0.5165	-0.011	0.2873	5.0117	3.484	-15.5493
26	3.0099	0.4208	0.5351	5.3519	2.399	5.6371	0.1613	-0.1506	-0.3606	0.1126	-0.0919	0.2413	0.11	-0.4291	-0.0343	0.0881	0.0143	0.0109	0.1556	0.0929	0.1904	-4.4811	-20.7101	-29.2546
27	0.7551	-0.2687	-0.0698	2.67	1.6527	2.1924	0.0224	-0.16	-0.0763	0.3294	0.0371	-0.004	0.2525	0.0125	-0.0752	0.2171	-0.0024	-0.0401	0.1948	0.0229	0.1012	33.0236	-14.5105	-0.0004
28	1.3273	-1.4883	-0.1434	5.431	0.5882	2.0326	0.0297	-0.2463	-0.0248	-0.1354	-0.0419	0.5191	-0.5893	-0.5429	0.1448	0.3256	0.0958	0.0008	0.3518	-0.0723	0.1594	23.9606	5.949	7.3974
29	1.3524	0.0347	0.3332	1.1204	-0.0964	1.5186	-0.1025	0.01	0.4063	0.0263	-0.0059	-0.0944	-0.6001	0.2951	0.0699	0.3624	-0.0904	-0.0299	0.2359	-0.0342	0.2208	36.7837	11.3728	-5.2362
30	1.1449	0.0651	0.4904	1.0051	0.101	1.5121	0.0236	-0.142	0.1934	0.118	-0.0394	0.0377	-0.327	-0.0235	-0.005	0.2109	0.0069	0.001	0.0963	-0.0155	0.1088	25.4873	-0.5484	-10.7273
31	3.1732	0.1537	-1.1749	0.7951	-0.3087	3.0649	0.0934	-0.3412	0.3058	0.0987	0.0538	0.0137	-0.4175	0.0367	-0.0506	0.2112	-0.02	-0.0549	0.1599	0.0093	0.1973	26.1602	-0.2691	-18.9969

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 57 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 58 through 113 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 114 through 151 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 152 through 192 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 193 through 277 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 278 through 322 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 323 through 375 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 376 through 397 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 6 through 35 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 36 through 57 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 58 through 93 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 94 through 219 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 220 through 240 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 241 through 277 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 278 through 318 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 319 through 375 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 376 through 394 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid -7 through 18 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 19 through 57 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 58 through 113 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 114 through 233 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 234 through 252 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 253 through 353 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 354 through 375 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 376 through 397 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 6 through 35 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 36 through 58 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 59 through 192 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 193 through 353 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 354 through 397 )

-
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

-
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

-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

-
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