PDB-4uab: Crystal structure of a TRAP periplasmic solute binding protein fr...

ID or keywords:

Entry

Database: PDB / ID: 4uab

Title

Crystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0678), Target EFI-501078, with bound ethanolamine

Components

Twin-arginine translocation pathway signal

Keywords

TRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

transmembrane transport
Similarity search - Function

Biological species

Chromohalobacter salexigens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.4 Å

Authors

Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...

History

Deposition	Aug 8, 2014	Deposition site: RCSB / Processing site: RCSB
Supersession	Sep 3, 2014	ID: 4N5W
Revision 1.0	Sep 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 25, 2015	Group: Database references
Revision 1.2	Aug 26, 2015	Group: Other
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Refinement description Category: pdbx_audit_support / pdbx_struct_oper_list / software Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4	Nov 22, 2017	Group: Refinement description / Category: software
Revision 2.0	Dec 25, 2019	Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 3.0	Nov 15, 2023	Group: Atomic model / Data collection / Database references Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.1	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4uab.cif.gz	386.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4uab.ent.gz	321.3 KB	Display	PDB format
PDBx/mmJSON format	4uab.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4uab_validation.pdf.gz	451.2 KB	Display	wwPDB validaton report
Full document	4uab_full_validation.pdf.gz	453.9 KB	Display
Data in XML	4uab_validation.xml.gz	29.4 KB	Display
Data in CIF	4uab_validation.cif.gz	44.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ua/4uab ftp://data.pdbj.org/pub/pdb/validation_reports/ua/4uab	HTTPS FTP

-
Related structure data

Related structure data	4ln5C 4mcoC 4mevC 4mhfC 4mijC 4mncC 4mniC 4mx6C 4n15C 4n17C 4n4uC 4n6dC 4n6kC 4n8gC 4n8yC 4n91C 4napC 4nf0C 4ng7C 4nguC 4nhbC 4nn3C 4nq8C 4nx1C 4o7mC 4o8mC 4o94C 4oa4C 4oanC 4ovpC 4ovqC 4ovrC 4ovsC 4ovtC 4p1eC 4p1lC 4p3lC 4p47C 4p56C 4p8bC 4p9kC 4pafC 4paiC 4pakC 4pbhC 4pbqC 4pc9C 4pcdC 4pddC 4pdhC 4pe3C 4petC 4pf6C 4pf8C 4pfbC 4pfiC 4pfrC 4pgnC 4pgpC C: citing same article (ref.)
Similar structure data	4xf5-d 3moh-1 2hzl-d 4d97-2 4d8w-1 2hzk-2 6i6x-2 4d96-2 3n3m-d 3w82-1 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: EFI-510078

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2)

Deposited unit

A: Twin-arginine translocation pathway signal

B: Twin-arginine translocation pathway signal

hetero molecules

80.5 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)	122.606, 51.117, 112.054
Angle α, β, γ (deg.)	90.000, 116.270, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-534- HOH

#1: Protein	Twin-arginine translocation pathway signal Mass: 40115.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / Gene: Csal_0678 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1QZR9
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-ETA / ETHANOLAMINE Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₇NO
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein (29.1 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.1 M Magnesium Chloride 0.1 M MES pH 6.5 30 %(w/v) PEG 400); Cryoprotection (Reservoir)

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2013 / Details: MIRRORS

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.4→100.485 Å / Num. all: 119470 / Num. obs: 119470 / % possible obs: 97.4 % / Redundancy: 6.3 % / B_iso Wilson estimate: 13.64 Å² / R_pim(I) all: 0.036 / R_rim(I) all: 0.093 / R_sym value: 0.071 / Net I/av σ(I): 7.546 / Net I/σ(I): 13 / Num. measured all: 748645

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_sym value	Net I/σ(I) obs	% possible all
1.4-1.48	5.2	0.712	1.1	87367	16689	0.353	0.712	2	93.4
1.48-1.57	5.6	0.449	1.7	90016	15969	0.216	0.449	3.2	95
1.57-1.67	5.9	0.281	2.8	90234	15357	0.135	0.281	5	96.8
1.67-1.81	6.2	0.193	4	90028	14581	0.092	0.193	7.3	98.4
1.81-1.98	6.5	0.123	6.2	87837	13497	0.059	0.123	11.6	99.4
1.98-2.21	6.8	0.083	8.8	83921	12345	0.041	0.083	17.9	99.8
2.21-2.56	7	0.066	10.6	76672	10885	0.033	0.066	23	99.9
2.56-3.13	7.2	0.055	11.9	66340	9196	0.028	0.055	28.9	99.8
3.13-4.43	7.1	0.046	14.6	51256	7174	0.022	0.046	35.7	99.5
4.43-60.89	6.6	0.04	16.3	24974	3777	0.023	0.04	34.4	94.1

-
Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
SCALA	3.3.20	data scaling
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.4→31.284 Å / FOM work R set: 0.8665 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.206	6006	5.03 %
R_work	0.1823	113444	-
obs	0.1835	119450	97.41 %

Solvent computation

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

Displacement parameters

B_iso max: 62.82 Å² / B_iso mean: 21.47 Å² / B_iso min: 6.31 Å²

Refinement step

Cycle: final / Resolution: 1.4→31.284 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5101	0	20	572	5693
B_iso mean	-	-	14.37	29.03	-
Num. residues	-	-	-	-	629

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5292
X-RAY DIFFRACTION	f_angle_d	1.225	7196
X-RAY DIFFRACTION	f_chiral_restr	0.076	743
X-RAY DIFFRACTION	f_plane_restr	0.008	935
X-RAY DIFFRACTION	f_dihedral_angle_d	13.952	1890

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4-1.4159	0.3103	196	0.2967	3546	3742	92
1.4159-1.4326	0.3093	172	0.2809	3588	3760	93
1.4326-1.45	0.284	212	0.2672	3639	3851	94
1.45-1.4684	0.2703	192	0.2514	3631	3823	94
1.4684-1.4877	0.265	205	0.2412	3656	3861	95
1.4877-1.5081	0.2659	182	0.2293	3637	3819	94
1.5081-1.5296	0.241	211	0.2203	3656	3867	96
1.5296-1.5525	0.2533	202	0.2149	3680	3882	95
1.5525-1.5767	0.2491	203	0.2052	3707	3910	96
1.5767-1.6026	0.2298	175	0.1949	3715	3890	96
1.6026-1.6302	0.2028	179	0.1886	3798	3977	97
1.6302-1.6599	0.2049	203	0.1817	3757	3960	97
1.6599-1.6918	0.2184	188	0.1824	3755	3943	98
1.6918-1.7263	0.2047	218	0.1849	3777	3995	98
1.7263-1.7638	0.2031	215	0.1862	3815	4030	98
1.7638-1.8049	0.2207	203	0.1815	3815	4018	99
1.8049-1.85	0.218	216	0.1803	3844	4060	99
1.85-1.9	0.2196	217	0.1762	3848	4065	99
1.9-1.9559	0.2179	179	0.1746	3872	4051	100
1.9559-2.019	0.1913	195	0.1761	3858	4053	100
2.019-2.0912	0.2094	192	0.1754	3873	4065	100
2.0912-2.1749	0.2008	227	0.1726	3862	4089	100
2.1749-2.2739	0.2048	203	0.1705	3888	4091	100
2.2739-2.3937	0.1932	193	0.1676	3909	4102	100
2.3937-2.5436	0.1907	205	0.1601	3904	4109	100
2.5436-2.7399	0.1969	201	0.1707	3897	4098	100
2.7399-3.0154	0.2004	194	0.1735	3915	4109	100
3.0154-3.4513	0.1805	197	0.1761	3913	4110	100
3.4513-4.3464	0.1818	236	0.1702	3884	4120	99
4.3464-31.2915	0.207	195	0.1883	3805	4000	94

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	1.298	0.0473	0.5599	0.5845	-0.8181	1.4175	0.0065	-0.3468	0.4075	0.1363	0.0766	-0.0348	-0.542	0.0986	-0.0085	0.2631	-0.1197	0.0482	0.2059	-0.0941	0.2483	10.9384	13.0652	32.9109
2	2.9569	-0.2124	-0.6157	1.3729	-0.3542	2.1775	0.0986	-0.4137	0.2748	0.287	0.222	-0.1145	-0.5067	0.3416	-0.1705	0.3199	-0.0505	0.0775	0.1609	-0.1026	0.267	4.067	15.5942	39.1537
3	0.5991	-0.15	-0.0026	0.848	0.0772	1.0758	0.0501	-0.1659	0.1677	0.1355	0.1235	-0.1885	-0.0799	0.5811	-0.1207	0.1324	-0.0484	-0.0038	0.2783	-0.0838	0.1835	16.4306	-0.2679	30.9338
4	1.198	0.2589	0.0981	0.9426	0.0308	0.7655	0.0039	-0.039	-0.0167	0.0077	-0.0112	-0.105	0.1024	0.5702	0.0242	0.0766	-0.0051	0.0028	0.2255	-0.0387	0.1355	14.7027	-2.4837	25.2806
5	0.6937	-0.4111	-1.1192	1.4446	-0.4078	3.2307	0.1653	0.1638	-0.1208	-0.2276	-0.0982	-0.1531	0.2227	0.7936	0.0924	0.1197	-0.0263	0.0292	0.4821	-0.0835	0.1617	23.8449	-3.267	12.1109
6	1.2433	0.2591	-0.2956	0.0998	0.0148	0.6318	0.1099	0.2647	0.1679	-0.1538	-0.0114	-0.018	-0.5366	0.5698	-0.0299	0.1824	-0.196	0.0532	0.3665	-0.0133	0.1672	17.2152	9.0338	12.4529
7	0.8082	0.1662	0.5247	1.0852	0.2092	1.3657	0.0507	-0.2288	0.0613	0.2312	0.0788	-0.1597	-0.043	0.4559	-0.0725	0.1246	-0.0551	-0.0203	0.278	-0.0663	0.1209	12.5407	1.5335	35.0922
8	1.7533	0.3083	-0.037	0.6548	0.7863	4.723	0.007	-0.1151	0.0975	0.0478	0.0462	0.0047	-0.188	0.1296	-0.0475	0.111	-0.0237	0.0089	0.0694	-0.007	0.1349	1.0723	3.9512	28.1999
9	1.1467	-0.204	0.7159	0.8382	-1.1968	2.6714	0.1149	0.3049	-0.2075	-0.2988	0.0066	0.0312	0.4447	0.4343	-0.1321	0.1802	0.0385	-0.0081	0.2773	-0.0614	0.1692	16.7434	-10.1316	11.7449
10	5.4033	0.771	2.3372	1.1506	0.4889	2.398	0.0538	0.1132	-0.4811	-0.0396	0.0689	-0.0311	0.3103	0.2255	-0.1488	0.181	0.047	-0.004	0.1266	-0.0236	0.2005	8.459	-18.0013	24.1676
11	2.1137	-0.8548	-0.7237	2.8424	1.1712	1.2995	0.0315	-0.2536	0.1055	0.1732	0.043	-0.1472	0.0393	-0.2283	-0.0579	0.121	-0.0048	0.0027	0.2205	0.0423	0.1029	-16.9103	-3.5527	41.5314
12	3.4719	1.2219	0.5328	1.8877	0.5257	1.8833	0.0915	-0.4457	0.1268	0.2282	-0.0399	0.0503	-0.122	-0.2769	-0.0479	0.1649	0.0171	0.0113	0.2174	0.0129	0.0881	-14.618	0.7752	46.0062
13	0.9297	-0.3271	0.3229	0.6796	0.3102	1.4054	-0.0381	-0.1508	0.0833	0.0428	0.0204	0.1084	-0.0617	-0.4564	0.0348	0.1075	0.0006	-0.0006	0.2378	0.0391	0.1421	-23.5262	-1.4918	28.4755
14	1.3842	-0.1715	0.0384	0.6121	0.0877	1.5851	0.0091	0.0308	0.0546	-0.012	0.0402	0.028	0.0169	-0.198	-0.0405	0.0719	-0.0178	0.0037	0.0843	0.0289	0.0805	-16.0096	-3.0224	23.6484
15	2.7962	-0.9981	0.4064	3.1579	-0.3442	1.1538	0.3763	0.4521	-0.3982	-0.6586	-0.0243	0.3362	0.6209	-0.5362	-0.071	0.1813	-0.2662	-0.0288	0.311	0.0784	0.1486	-25.8589	-19.0203	19.145
16	0.615	0.8597	1.2178	1.9733	2.4829	3.2162	0.1329	0.0506	-0.1833	0.5443	0.0038	0.0936	0.9743	-0.7452	0.0609	0.3088	-0.2009	0.0058	0.3828	0.0958	0.2226	-25.5124	-20.1188	33.1848
17	1.3071	-0.109	0.1482	1.4138	0.164	1.6249	0.0997	-0.0994	-0.1214	0.1473	-0.0511	0.0417	0.2407	-0.3626	-0.0159	0.1216	-0.082	-0.0143	0.135	0.075	0.1079	-17.2901	-10.7757	31.0552
18	1.6401	-0.2979	-0.1805	2.8152	1.0345	2.0799	0.0328	-0.1085	0.005	0.031	0.0717	-0.0127	0.0266	-0.0127	-0.0738	0.0756	-0.0086	0.0012	0.0572	0.0243	0.0841	-5.7327	-3.9539	33.0668
19	2.2459	-0.9096	0.3642	1.7074	-0.4435	1.2271	0.2155	0.4391	-0.2006	-0.2207	-0.2184	-0.04	0.3982	-0.1725	-0.0311	0.1911	-0.0872	-0.0271	0.2346	0.016	0.1557	-17.9483	-16.9083	13.3563
20	7.2108	-1.706	-0.7472	0.9233	0.3177	2.2847	0.0311	0.245	0.1657	-0.053	0.0893	0.0018	-0.0237	-0.0794	-0.1257	0.1189	-0.028	-0.0124	0.1427	0.0388	0.1152	-11.0451	-1.6256	10.4001

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 33 through 51 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 71 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 132 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 133 through 167 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 168 through 189 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 190 through 234 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 235 through 257 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 258 through 289 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 290 through 321 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 322 through 347 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 34 through 51 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 52 through 78 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 79 through 120 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 121 through 167 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 168 through 189 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 190 through 206 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 207 through 257 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 258 through 289 )	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 290 through 320 )	B
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 321 through 347 )	B

-
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