PDB-4mgr: The crystal structure of Bacillus subtilis GabR, an autorepressor...

ID or keywords:

Entry

Database: PDB / ID: 4mgr

Title

The crystal structure of Bacillus subtilis GabR, an autorepressor and PLP- and GABA-dependent transcriptional activator of gabT

Components

HTH-type transcriptional regulatory protein GabR

Keywords

TRANSCRIPTION REGULATOR / Winged Helix Turn Helix / type-I aminotransferase / PLP Binding / DNA Binding

Function / homology

Function and homology information

transaminase activity / biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Wu, R. / Edayathumangalam, R. / Garcia, R. / Wang, Y. / Wang, W. / Kreinbring, C.A. / Bach, A. / Liao, J. / Stone, T. / Terwilliger, T. ...

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT.
Authors: Edayathumangalam, R. / Wu, R. / Garcia, R. / Wang, Y. / Wang, W. / Kreinbring, C.A. / Bach, A. / Liao, J. / Stone, T.A. / Terwilliger, T.C. / Hoang, Q.Q. / Belitsky, B.R. / Petsko, G.A. / Ringe, D. / Liu, D.

History

Deposition	Aug 28, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 5, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4mgr.cif.gz	776.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4mgr.ent.gz	648 KB	Display	PDB format
PDBx/mmJSON format	4mgr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4mgr_validation.pdf.gz	497.4 KB	Display	wwPDB validaton report
Full document	4mgr_full_validation.pdf.gz	541.1 KB	Display
Data in XML	4mgr_validation.xml.gz	73.3 KB	Display
Data in CIF	4mgr_validation.cif.gz	99.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/4mgr ftp://data.pdbj.org/pub/pdb/validation_reports/mg/4mgr	HTTPS FTP

-
Related structure data

Related structure data	4n0bC C: citing same article (ref.)
Similar structure data	5h1b-d 5ups-d 4tv7-2 3csn-2 4tv7-1 5djq-3 5h1c-d 3mk7-4 5djq-2 7c99-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) 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	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: HTH-type transcriptional regulatory protein GabR

B: HTH-type transcriptional regulatory protein GabR

C: HTH-type transcriptional regulatory protein GabR

D: HTH-type transcriptional regulatory protein GabR

hetero molecules

225 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: HTH-type transcriptional regulatory protein GabR

B: HTH-type transcriptional regulatory protein GabR

hetero molecules

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

2

C: HTH-type transcriptional regulatory protein GabR

D: HTH-type transcriptional regulatory protein GabR

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.930, 101.360, 213.200
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	HTH-type transcriptional regulatory protein GabR Mass: 56068.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: gabR, ycnF, BSU03890 / Production host: Escherichia coli (E. coli) / References: UniProt: P94426
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₅N₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.41 Å³/Da / Density % sol: 48.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 33% PEG400, 200mM calcium acetate and 200mM imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 20, 2010
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.43→49.3 Å / Num. all: 82827 / Num. obs: 80839 / % possible obs: 97.6 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / R_merge(I) obs: 0.118 / Net I/σ(I): 10.6

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→49.3 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 24.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2437	3460	5.07 %	random
R_work	0.1942	-	-	-
obs	0.1967	68190	95.56 %	-
all	-	71180	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 46.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→49.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15243	0	60	467	15770

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	15593
X-RAY DIFFRACTION	f_angle_d	1.125	21001
X-RAY DIFFRACTION	f_dihedral_angle_d	16.803	5996
X-RAY DIFFRACTION	f_chiral_restr	0.084	2291
X-RAY DIFFRACTION	f_plane_restr	0.004	2719

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 (%)
2.55-2.5849	0.3351	129	0.2787	2406	X-RAY DIFFRACTION	90
2.5849-2.6219	0.3237	150	0.2464	2384	X-RAY DIFFRACTION	90
2.6219-2.661	0.3245	126	0.2591	2436	X-RAY DIFFRACTION	91
2.661-2.7026	0.2997	137	0.2499	2438	X-RAY DIFFRACTION	91
2.7026-2.7469	0.3017	122	0.2411	2507	X-RAY DIFFRACTION	93
2.7469-2.7942	0.3179	124	0.2437	2459	X-RAY DIFFRACTION	92
2.7942-2.845	0.2986	138	0.2396	2485	X-RAY DIFFRACTION	92
2.845-2.8998	0.3511	134	0.2265	2470	X-RAY DIFFRACTION	93
2.8998-2.9589	0.3375	142	0.2383	2475	X-RAY DIFFRACTION	92
2.9589-3.0233	0.3112	136	0.2317	2474	X-RAY DIFFRACTION	92
3.0233-3.0936	0.2643	139	0.2213	2537	X-RAY DIFFRACTION	94
3.0936-3.1709	0.2479	151	0.2211	2511	X-RAY DIFFRACTION	94
3.1709-3.2567	0.2903	141	0.2164	2574	X-RAY DIFFRACTION	96
3.2567-3.3525	0.2348	132	0.204	2612	X-RAY DIFFRACTION	97
3.3525-3.4606	0.2568	145	0.2034	2659	X-RAY DIFFRACTION	98
3.4606-3.5843	0.2671	132	0.1966	2679	X-RAY DIFFRACTION	99
3.5843-3.7278	0.2362	150	0.192	2690	X-RAY DIFFRACTION	100
3.7278-3.8974	0.2174	126	0.1814	2712	X-RAY DIFFRACTION	100
3.8974-4.1027	0.2226	154	0.1735	2703	X-RAY DIFFRACTION	100
4.1027-4.3596	0.1836	137	0.157	2725	X-RAY DIFFRACTION	100
4.3596-4.696	0.1797	142	0.1557	2711	X-RAY DIFFRACTION	100
4.696-5.1681	0.232	143	0.1655	2736	X-RAY DIFFRACTION	99
5.1681-5.9149	0.2527	123	0.196	2778	X-RAY DIFFRACTION	99
5.9149-7.448	0.246	142	0.2044	2749	X-RAY DIFFRACTION	99
7.448-49.3153	0.2048	165	0.1686	2820	X-RAY DIFFRACTION	97

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	2.7707	-0.2975	-0.3011	2.8228	-0.3602	2.7124	-0.0589	0.4601	-0.8158	-0.4013	-0.1315	0.0524	0.4914	-0.0228	0.1508	0.3698	-0.0841	0.0564	0.2906	-0.1361	0.3752	20.4307	-32.2313	-10.2007
2	0.7447	0.3586	-1.0132	1.1735	0.7351	2.35	0.062	0.3093	-0.1157	-0.3396	-0.1522	-0.281	-0.013	0.4127	0.0467	0.4826	0.0531	0.2051	0.323	0.0008	0.4557	23.0894	13.1491	-3.7583
3	3.1048	-1.1568	-1.0597	1.8125	0.8485	1.4089	0.1609	0.2668	0.0494	-0.1318	-0.1299	0.0255	-0.257	-0.1692	-0.0268	0.3641	0.036	0.0789	0.1534	0.0157	0.149	4.9046	19.9533	11.1643
4	2.2042	-1.5059	0.1302	2.1813	0.1822	2.5925	0.4364	0.7083	0.1191	-0.7426	-0.4624	0.0154	-0.4855	-0.4295	0.0817	0.6273	0.1736	0.0898	0.4217	-0.0014	0.1948	5.6056	22.2716	-6.3933
5	1.0046	0.5392	-0.4622	2.9624	-1.0576	4.6833	0.2781	-1.0042	0.685	0.5854	-0.488	-0.127	-0.84	1.6043	0.1442	0.9576	0.1201	0.4234	-0.1875	-0.1419	0.7335	12.1509	47.4815	12.2631
6	0.7152	0.1923	0.0672	1.4202	0.1326	-0.3191	0.5707	0.0966	0.4665	-0.1318	-0.159	-0.6874	-0.2229	0.006	-0.435	0.6993	0.0869	0.1471	0.4017	0.0217	0.3947	22.3324	11.9156	17.5546
7	1.9931	0.9351	2.5679	2.5069	-1.1775	4.0673	-1.2145	2.8668	3.3045	-1.9385	-0.8124	-1.3181	-1.7976	1.8431	0.5082	0.973	-0.0296	0.4115	0.2708	-0.2197	0.3999	23.3945	6.8803	-11.4863
8	1.1927	-0.4389	-0.5386	3.2548	0.409	2.5889	-0.0029	-0.1424	-0.1309	-0.2007	-0.0147	0.3715	-0.0207	-0.0942	0.0121	0.0781	0.0055	-0.005	0.1484	0.0058	0.1995	10.7192	-16.2351	3.2201
9	3.9793	-0.3331	-1.0491	3.4071	0.2011	2.2246	0.4657	-0.3864	0.2589	-0.5311	-0.2126	-0.06	-0.3058	0.1311	-0.1886	0.3998	0.0682	0.1235	0.1372	-0.031	0.1583	14.7893	-1.7913	-4.5823
10	2.0592	-0.7902	1.4298	3.6614	-0.2262	2.8256	-0.0929	-0.6131	0.2442	0.3328	0.174	-0.4382	-0.2734	0.2344	-0.0537	0.1339	0.1139	-0.0574	0.4464	-0.0984	0.2249	32.1008	-16.5237	17.8458
11	2.5799	-1.1739	0.548	3.995	-0.6022	2.4376	-0.2693	-0.3926	0.2059	0.3457	0.0111	0.3145	-0.6983	-0.5964	0.1995	0.2565	0.1301	0.0936	0.2692	-0.0121	0.2363	22.8824	34.2359	-29.7324
12	2.8199	-0.7417	0.7302	0.5861	0.0661	0.3546	-0.5599	-0.1728	-0.0079	0.2592	0.2846	-0.0057	-0.1594	0.2431	-0.0379	0.4578	-0.1387	-0.0278	0.3835	-0.0675	0.298	27.4668	-12.9739	-31.2847
13	2.4596	0.3081	0.619	2.2554	0.1673	1.9656	-0.0236	0.1069	0.1032	-0.4002	0.0899	0.0546	-0.1547	-0.0681	-0.0516	0.1923	-0.0002	0.0881	0.165	-0.006	0.0774	21.8527	-16.9914	-56.98
14	2.6147	-0.0994	2.2559	3.0183	0.3674	2.0308	-0.1487	0.029	0.223	0.1055	0.2972	0.0636	-0.2582	0.0568	-0.0524	0.1886	0.0309	0.0933	0.1407	-0.0294	0.1766	32.1722	-9.4433	-48.3664
15	3.6271	-0.0696	-1.1062	1.7358	-0.4508	2.4115	-0.0921	-0.052	0.195	0.1019	0.109	0.2705	0.1918	-0.5725	-0.0149	0.2181	-0.1034	0.0685	0.2678	-0.0353	0.2311	5.3136	-22.826	-36.5141
16	2.7026	-0.5359	0.4034	2.8038	-0.4182	3.7501	-0.0147	0.3498	-0.6438	-0.5997	-0.0049	0.0216	0.6066	0.0629	-0.0632	0.4261	-0.044	0.0076	0.1967	-0.0494	0.2871	26.6627	-45.6737	-53.3418
17	1.7859	1.5817	-0.1543	3.2963	-0.002	0.8095	0.1189	0.4978	-0.139	-0.6433	0.1778	-0.6351	-0.17	0.376	-0.1316	0.7394	-0.1134	0.1996	0.5478	-0.1247	0.6173	32.7807	-23.7747	-65.287
18	1.1824	-0.7301	0.5914	1.7678	0.4981	0.539	-0.1745	-0.3528	-0.7569	0.2787	-0.0436	-0.4951	0.5108	0.1324	0.2793	0.4877	-0.07	0.0389	0.2783	0.0697	0.3784	34.8789	0.2269	-33.9834
19	1.1612	1.6904	-0.3802	3.7427	-0.2796	2.4576	-0.0211	0.0557	0.1045	0.118	-0.1042	0.3856	-0.0067	-0.0241	0.1312	0.1314	0.0652	0.0338	0.1351	-0.0292	0.1823	19.29	10.6197	-42.0472
20	2.4656	0.2374	-0.3394	3.5967	0.8248	2.6642	-0.0447	0.2916	-0.0041	-0.2772	-0.0254	0.2616	-0.3187	-0.2226	0.0378	0.1241	0.0687	-0.0121	0.1451	0.0427	0.1115	22.1535	21.8358	-48.3752
21	3.2363	-0.497	3.1023	3.5194	-0.4108	4.3747	0.0432	0.2101	0.0099	0.1482	0.0331	0.2639	0.2514	0.1654	-0.077	0.2387	-0.0355	0.1013	0.1409	0.0292	0.1449	21.7546	3.6981	-37.4141
22	1.7956	0.2053	-1.1461	2.1384	0.0467	3.9896	-0.0517	0.1355	0.0067	-0.0987	-0.0268	-0.3743	-0.1169	0.3152	0.089	0.1159	-0.0587	0.0672	0.2125	-0.0044	0.2507	46.1154	19.9217	-47.2545
23	6.2016	2.203	-1.1359	2.6337	0.5599	1.4328	-0.1898	0.3042	-0.2926	-0.1537	0.0468	-0.1193	0.0062	0.5288	0.1443	0.1999	0.0406	0.1168	0.2835	0.0062	0.2912	48.525	19.2359	-54.6349

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 104 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 105 through 151 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 152 through 320 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 321 through 469 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 76 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 77 through 123 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 124 through 151 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 152 through 309 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 310 through 358 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 359 through 472 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 104 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 105 through 140 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 141 through 309 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 310 through 358 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 359 through 475 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 76 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 77 through 104 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 105 through 151 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 152 through 205 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 206 through 309 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 310 through 358 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 359 through 431 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 432 through 472 )

-
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