PDB-5er6: Crystal structure of an oxidoreductase from Brucella ovis

ID or keywords:

Entry

Database: PDB / ID: 5er6

Title

Crystal structure of an oxidoreductase from Brucella ovis

Components

Oxidoreductase, short chain dehydrogenase/reductase family

Keywords

OXIDOREDUCTASE / SSGCID / short chain dehydrogenase/reductase family /

Brucella ovis /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

Brucella ovis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of an oxidoreductase from Brucella ovis
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Nov 13, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	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	5er6.cif.gz	374.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5er6.ent.gz	304.9 KB	Display	PDB format
PDBx/mmJSON format	5er6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/er/5er6 ftp://data.pdbj.org/pub/pdb/validation_reports/er/5er6	HTTPS FTP

-
Related structure data

Related structure data	4gh5S S: Starting model for refinement
Similar structure data	2ewm-1 6ux3-d 5xtf-1 3vc7-4 6ihi-d 5wva-1 6oz7-1 6f9q-d 5ff9-d 5u2w-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	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Oxidoreductase, short chain dehydrogenase/reductase family

B: Oxidoreductase, short chain dehydrogenase/reductase family

C: Oxidoreductase, short chain dehydrogenase/reductase family

D: Oxidoreductase, short chain dehydrogenase/reductase family

hetero molecules

104 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)	52.010, 94.810, 99.490
Angle α, β, γ (deg.)	90.000, 99.540, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Oxidoreductase, short chain dehydrogenase/reductase family / Mass: 25754.584 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) (bacteria) Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: BOV_A0028 / Plasmid: BrovA.00010.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3ATY4
#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1128 / 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: 2.36 Å³/Da / Density % sol: 48 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: JCSG+ H10: 200mM Ammonium sulfate, 100mM BIS-Tris pH5.5 25% PEG3350; BrovA.00010.a.B1.PS02326 at 24.76mg/Ml; 15% EG; tray 261921h10; puck ixr1-8

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2015

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 135447 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.26 % / B_iso Wilson estimate: 12.79 Å² / R_merge F obs: 0.997 / R_merge(I) obs: 0.078 / R_rim(I) all: 0.089 / Χ²: 0.997 / Net I/σ(I): 12.18 / Num. measured all: 576794

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.55-1.59	4.29	0.803	0.526	2.88	42277	10161	9845	0.601	96.9
1.59-1.63		0.856	0.44	3.41	41276	9918	9618	0.504	97
1.63-1.68		0.882	0.37	4.07	40181	9615	9370	0.423	97.5
1.68-1.73		0.917	0.304	4.89	39055	9319	9096	0.347	97.6
1.73-1.79		0.942	0.251	5.78	38239	9111	8901	0.287	97.7
1.79-1.85		0.961	0.203	7	36930	8775	8600	0.232	98
1.85-1.92		0.972	0.163	8.55	35465	8435	8278	0.186	98.1
1.92-2		0.984	0.126	10.63	34400	8176	8045	0.144	98.4
2-2.09		0.987	0.106	12.19	32827	7810	7690	0.122	98.5
2.09-2.19		0.99	0.089	14.42	31348	7452	7357	0.102	98.7
2.19-2.31		0.992	0.078	16.1	30049	7150	7063	0.089	98.8
2.31-2.45		0.993	0.071	17.35	28349	6705	6657	0.081	99.3
2.45-2.62		0.994	0.065	18.76	26679	6346	6298	0.075	99.2
2.62-2.83		0.994	0.06	20.42	24822	5899	5860	0.068	99.3
2.83-3.1		0.995	0.054	22.4	22786	5437	5410	0.062	99.5
3.1-3.47		0.996	0.049	24.21	20540	4929	4912	0.056	99.7
3.47-4		0.996	0.046	26.01	18096	4362	4353	0.052	99.8
4-4.9		0.996	0.042	27.08	15309	3672	3666	0.049	99.8
4.9-6.93		0.996	0.042	26.61	11910	2862	2856	0.048	99.8

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
PHENIX	dev_2219	refinement
PDB_EXTRACT	3.15	data extraction
Coot		model building
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4GH5

4gh5

Resolution: 1.55→50 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.167	2000	1.48 %	Random selection
R_work	0.1456	133447	-	-
obs	0.1459	135447	98.34 %	-

Solvent computation

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

Displacement parameters

B_iso max: 73.84 Å² / B_iso mean: 17.8481 Å² / B_iso min: 5.27 Å²

Refinement step

Cycle: final / Resolution: 1.55→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6882	0	56	1135	8073
B_iso mean	-	-	35.93	32.44	-
Num. residues	-	-	-	-	969

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7259
X-RAY DIFFRACTION	f_angle_d	0.767	9894
X-RAY DIFFRACTION	f_chiral_restr	0.057	1198
X-RAY DIFFRACTION	f_plane_restr	0.005	1301
X-RAY DIFFRACTION	f_dihedral_angle_d	11.36	4320

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 (%)
1.55-1.5887	0.2333	140	0.2139	9330	X-RAY DIFFRACTION	97
1.5887-1.6317	0.2014	141	0.1929	9391	X-RAY DIFFRACTION	97
1.6317-1.6797	0.238	141	0.1785	9427	X-RAY DIFFRACTION	97
1.6797-1.7339	0.1889	141	0.1674	9412	X-RAY DIFFRACTION	98
1.7339-1.7959	0.1906	141	0.1573	9435	X-RAY DIFFRACTION	98
1.7959-1.8678	0.1762	142	0.1542	9464	X-RAY DIFFRACTION	98
1.8678-1.9528	0.18	142	0.1543	9502	X-RAY DIFFRACTION	98
1.9528-2.0557	0.1573	143	0.1378	9526	X-RAY DIFFRACTION	98
2.0557-2.1845	0.155	144	0.137	9573	X-RAY DIFFRACTION	99
2.1845-2.3532	0.1699	144	0.1377	9602	X-RAY DIFFRACTION	99
2.3532-2.59	0.1699	144	0.1426	9600	X-RAY DIFFRACTION	99
2.59-2.9647	0.1649	144	0.1432	9645	X-RAY DIFFRACTION	99
2.9647-3.7349	0.1543	146	0.1322	9739	X-RAY DIFFRACTION	100
3.7349-50	0.1419	147	0.1355	9801	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	1.3353	1.0748	1.2065	0.902	1.0234	1.1783	0.0033	-0.073	0.0091	-0.0546	0.0279	-0.0439	-0.1542	0.0393	-0.0544	0.0537	0.0076	-0.0088	0.0597	-0.0014	0.0776	-22.0537	18.4883	24.2922
2	2.3963	-0.0538	1.3866	1.7595	0.2367	1.7893	-0.0102	-0.0301	0.068	-0.0913	0.0104	-0.0067	-0.2462	-0.0178	0.0037	0.0734	0.0057	-0.0053	0.0638	0.0084	0.0709	-26.0984	22.5095	24.2618
3	0.6981	-0.12	0.1873	2.1332	-1.7288	3.1087	-0.0811	-0.0438	0.0821	0.0428	0.0142	0.0444	-0.2041	-0.1834	-0.0072	0.0786	0.0212	-0.0162	0.0897	-0.0126	0.0953	-28.8212	21.5089	30.863
4	1.3585	-0.6135	0.7357	0.8849	-0.3928	1.0721	-0.0689	-0.0296	0.1703	0.0973	-0.0122	-0.0551	-0.0584	0.0012	0.0558	0.0546	-0.007	0.0039	0.0673	-0.0068	0.0982	-18.9436	11.5576	35.9058
5	0.3884	-0.3836	0.0406	0.4692	0.1759	0.6651	-0.0002	0.0013	0.0392	0.0075	0.0175	-0.008	-0.0241	0.0196	-0.0092	0.0447	-0.0094	-0.0017	0.0725	0.0133	0.0924	-19.1318	6.196	29.5358
6	0.9858	-0.1657	0.1384	1.146	0.0767	0.9654	0.0348	0.0019	0.0348	-0.0875	-0.0114	-0.0346	-0.0221	0.0477	-0.0052	0.0539	-0.0069	-0.0028	0.0455	-0.0047	0.0456	-14.2683	5.0775	16.9755
7	1.5034	-0.4	0.244	3.0519	0.5542	1.3562	0.0375	-0.0998	-0.0252	0.108	0.031	0.1718	0.0967	-0.1513	-0.0643	0.0938	0.0141	0.0196	0.0994	0.0429	0.0735	-9.965	-17.3608	52.5126
8	0.2635	-0.3284	0.2648	0.6537	-0.2271	0.5672	-0.0589	-0.0796	-0.0548	0.1113	0.072	0.0575	-0.0203	-0.064	-0.0066	0.0724	0.0109	0.0069	0.0899	0.0142	0.0858	-10.2855	-8.2228	48.1428
9	0.6599	-0.6516	0.2312	1.8904	-0.1359	0.9411	0.1252	-0.3241	-0.0481	0.1793	-0.0725	0.553	-0.0436	-0.4392	0.0146	0.1727	-0.0395	0.0437	0.2562	0.0123	0.2975	-24.7421	-22.3099	36.1416
10	1.483	0.1522	0.5618	1.049	-0.0041	1.4408	0.0575	-0.1103	-0.0351	0.0135	-0.0445	0.0961	0.1424	-0.0706	-0.0009	0.0701	0.0049	0.0075	0.0536	0.0037	0.0882	-8.6097	-19.6634	37.0701
11	1.381	0.4645	0.3186	1.5608	-0.0469	2.4321	0.0065	-0.002	-0.0227	-0.1491	-0.1375	0.1912	-0.0358	-0.3944	0.1617	0.1245	0.0198	-0.0446	0.1359	-0.0524	0.1088	-25.7339	-6.5351	-1.9225
12	0.7401	0.0768	0.6048	1.4099	-0.2049	0.8205	-0.0267	-0.023	0.0465	-0.3074	-0.1995	0.3151	-0.2007	-0.3471	0.0772	0.2215	0.0494	-0.0818	0.159	-0.0598	0.1495	-26.9892	-4.0245	-9.0134
13	0.7203	0.1123	0.4712	2.3282	0.2581	2.3395	0.0271	0.0869	-0.0249	-0.3521	0.0273	0.0054	0.3645	0.2944	-0.0805	0.1771	0.0183	-0.0071	0.1437	-0.0345	0.0795	-12.4929	-15.1988	-8.5957
14	0.3976	0.4606	0.7828	3.2243	-0.9303	2.7938	-0.105	0.1995	-0.0186	-0.4573	0.102	-0.147	-0.1673	0.227	-0.0022	0.1767	-0.0337	0.0132	0.1372	-0.0163	0.1016	-13.2589	-2.2001	-8.4412
15	0.5552	-0.1962	-0.1555	1.3979	-0.7836	1.9284	0.0204	0.0009	-0.1146	-0.0609	0.0126	0.1223	0.1539	-0.0318	-0.0402	0.1059	-0.0043	-0.0197	0.1098	-0.0189	0.1087	-15.5899	-16.6807	6.4375
16	1.6881	0.7608	0.0651	3.6123	-0.4304	1.5482	0.0063	-0.0114	-0.0393	-0.0937	0.0037	-0.0229	-0.016	0.1524	0.0163	0.0562	-0.0017	0.001	0.0721	-0.0087	0.0308	-9.1824	-5.0587	8.8709
17	1.0747	-0.3431	-0.5709	1.6733	-0.5863	0.869	-0.142	0.2077	-0.326	-0.1512	0.0642	0.4574	0.2936	-0.2733	0.047	0.1746	-0.0643	-0.0205	0.1699	-0.0234	0.3133	-31.9394	-13.5382	18.6708
18	0.9445	0.1329	-0.383	1.2322	-0.5361	1.8584	-0.0125	0.0341	-0.0937	-0.0656	-0.0128	0.1135	0.0401	-0.1319	0.0204	0.0663	0.0078	-0.0178	0.0667	-0.025	0.0895	-22.676	-1.6274	12.5675
19	0.7944	0.1576	0.1966	1.7242	-0.7806	0.4458	0.0342	0.0746	-0.0241	-0.1532	-0.0261	-0.1994	0.2626	0.2865	-0.0006	0.1791	0.0858	0.0121	0.1443	-0.0094	0.1417	6.4244	-35.0018	23.7861
20	0.9821	-0.6757	-0.1849	0.8215	-0.3186	0.8348	0.0435	-0.0235	-0.1487	-0.1433	-0.0216	-0.0303	0.404	0.26	-0.0299	0.3018	0.1125	-0.0025	0.177	-0.0232	0.1986	3.5781	-39.3833	17.8465
21	0.5484	-0.6358	0.3828	1.5903	-0.5782	1.1464	0.0764	0.0946	-0.0734	-0.227	-0.1263	-0.1895	0.2694	0.2109	0.0891	0.1557	0.0338	-0.0005	0.1272	-0.0238	0.1299	-2.0939	-26.587	11.5673
22	0.3232	0.3297	0.1048	3.3997	-0.8201	1.228	0.0671	0.0128	-0.0675	-0.033	-0.0052	0.1323	0.1701	0.029	-0.043	0.0836	0.0204	-0.014	0.0781	-0.0075	0.096	-6.5989	-24.5509	19.0227
23	0.342	-0.0291	0.392	1.0704	0.2106	1.1835	0.0057	0.044	-0.0391	-0.1536	-0.0022	-0.0323	0.0383	0.1017	-0.0339	0.0767	0.0175	0.0135	0.0887	0.0121	0.1099	-3.4598	-17.7627	23.7417
24	0.6272	-0.1778	0.2463	1.3674	-0.2011	0.8056	0.01	-0.0084	-0.1279	-0.0137	0.0137	-0.0821	0.1095	0.0424	-0.024	0.0607	0.0159	0.0077	0.0604	0.001	0.0877	-2.5236	-20.8451	31.0869

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 24 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 47 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 74 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 75 through 109 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 110 through 205 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 206 through 250 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 8 through 24 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 25 through 184 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 185 through 215 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 216 through 250 )	B
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 9 through 24 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 25 through 60 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 61 through 74 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 75 through 89 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 90 through 160 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 161 through 184 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 185 through 215 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 216 through 250 )	C
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 9 through 47 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 48 through 74 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 75 through 123 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 124 through 160 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 161 through 215 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 216 through 250 )	D

-
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