PDB-3vbe: Crystal structure of beta-cyanoalanine synthase in soybean

ID or keywords:

Entry

Database: PDB / ID: 3vbe

Title

Crystal structure of beta-cyanoalanine synthase in soybean

Components

beta-cyanoalnine synthase

Keywords

TRANSFERASE / beta-cyanoalanine synthase

Function / homology

Function and homology information

L-3-cyanoalanine synthase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / mitochondrion / cytoplasm
Similarity search - Function

Biological species

Glycine max (soybean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Yi, H. / Jez, J.M.

Citation

Journal: Plant Cell / Year: 2012
Title: Structure of Soybean beta-Cyanoalanine Synthase and the Molecular Basis for Cyanide Detoxification in Plants.
Authors: Yi, H. / Juergens, M. / Jez, J.M.

History

Deposition	Jan 2, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3vbe.cif.gz	491 KB	Display	PDBx/mmCIF format
PDB format	pdb3vbe.ent.gz	420.5 KB	Display	PDB format
PDBx/mmJSON format	3vbe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3vbe_validation.pdf.gz	474.9 KB	Display	wwPDB validaton report
Full document	3vbe_full_validation.pdf.gz	495.9 KB	Display
Data in XML	3vbe_validation.xml.gz	49 KB	Display
Data in CIF	3vbe_validation.cif.gz	67.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vb/3vbe ftp://data.pdbj.org/pub/pdb/validation_reports/vb/3vbe	HTTPS FTP

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Related structure data

Related structure data	3vc3C C: citing same article (ref.)
Similar structure data	5d84-1 5pzl-1 2jir-d 5pzo-1 4wti-d 4wtj-d 6j1f-2 4oow-2 4obc-d 4ju2-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (3)

Deposited unit

A: beta-cyanoalnine synthase

B: beta-cyanoalnine synthase

C: beta-cyanoalnine synthase

D: beta-cyanoalnine synthase

hetero molecules

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

1

A: beta-cyanoalnine synthase

B: beta-cyanoalnine synthase

hetero molecules

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

2

C: beta-cyanoalnine synthase

D: beta-cyanoalnine synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	190.323, 154.580, 70.800
Angle α, β, γ (deg.)	90.00, 101.89, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	beta-cyanoalnine synthase Mass: 37236.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Strain: Williams 82 / Gene: GLYMA09G39390, OAS-TL3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I1L6I6*PLUS, cysteine synthase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	LOCALIZATION PEPTIDE AT THE N-TERMINAL. NCBI SEQUENCE REFERENCE XP_003534555.1, RESIDUES 52-373

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.41 Å³/Da / Density % sol: 63.92 %
Crystal grow	Temperature: 279 K / pH: 6.2 Details: 10% (w/v) PEG-8000, 0.1 M Na/K phosphate, 0.2M NaCl, pH 6.2, vapor diffusion, hanging drop, temperature 279K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2010
Radiation	Monochromator: ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→100 Å / Num. obs: 68674 / % possible obs: 99.8 % / Redundancy: 4.8 % / R_merge(I) obs: 0.108 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 5 % / R_merge(I) obs: 0.667 / % possible all: 100

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→49.16 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.69 / σ(F): 1.33 / Phase error: 22.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.21	3462	5.06 %
R_work	0.167	-	-
obs	0.169	68418	99.2 %

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.66 Å² / k_sol: 0.34 e/Å³

Displacement parameters

B_iso mean: 53.66 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.0943 Å²	-0 Å²	1.1955 Å²
2-	-	-1.5118 Å²	-0 Å²
3-	-	-	1.4175 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→49.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9699	0	60	214	9973

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9928
X-RAY DIFFRACTION	f_angle_d	1.106	13438
X-RAY DIFFRACTION	f_dihedral_angle_d	14.267	3723
X-RAY DIFFRACTION	f_chiral_restr	0.072	1536
X-RAY DIFFRACTION	f_plane_restr	0.005	1736

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 (%)
2.5016-2.5359	0.3028	128	0.2321	2366	X-RAY DIFFRACTION	91
2.5359-2.5721	0.3432	129	0.2352	2574	X-RAY DIFFRACTION	99
2.5721-2.6105	0.2999	143	0.2169	2629	X-RAY DIFFRACTION	99
2.6105-2.6513	0.2611	121	0.2065	2592	X-RAY DIFFRACTION	99
2.6513-2.6948	0.2599	115	0.2046	2579	X-RAY DIFFRACTION	99
2.6948-2.7412	0.2741	124	0.2084	2645	X-RAY DIFFRACTION	99
2.7412-2.7911	0.2529	127	0.2198	2569	X-RAY DIFFRACTION	99
2.7911-2.8448	0.3178	145	0.2152	2617	X-RAY DIFFRACTION	100
2.8448-2.9028	0.2682	122	0.206	2589	X-RAY DIFFRACTION	99
2.9028-2.9659	0.2648	135	0.2	2616	X-RAY DIFFRACTION	100
2.9659-3.0349	0.2751	134	0.1899	2604	X-RAY DIFFRACTION	100
3.0349-3.1108	0.2407	143	0.1792	2595	X-RAY DIFFRACTION	100
3.1108-3.1949	0.2172	148	0.1809	2612	X-RAY DIFFRACTION	100
3.1949-3.2889	0.2332	147	0.1828	2608	X-RAY DIFFRACTION	100
3.2889-3.395	0.2275	131	0.1745	2637	X-RAY DIFFRACTION	100
3.395-3.5163	0.2485	149	0.1752	2601	X-RAY DIFFRACTION	100
3.5163-3.6571	0.2212	131	0.1634	2621	X-RAY DIFFRACTION	100
3.6571-3.8234	0.1756	156	0.1522	2601	X-RAY DIFFRACTION	100
3.8234-4.0249	0.1624	148	0.1388	2608	X-RAY DIFFRACTION	100
4.0249-4.277	0.1871	138	0.1347	2624	X-RAY DIFFRACTION	100
4.277-4.607	0.1524	148	0.1204	2610	X-RAY DIFFRACTION	100
4.607-5.0702	0.1745	155	0.1275	2626	X-RAY DIFFRACTION	100
5.0702-5.8028	0.1891	138	0.1711	2634	X-RAY DIFFRACTION	100
5.8028-7.3071	0.1904	152	0.1663	2620	X-RAY DIFFRACTION	100
7.3071-49.1649	0.1979	155	0.1677	2579	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	0.0444	-0.0337	-0.1619	0.1024	0.1887	0.9463	0.2023	-0.051	-0.0646	-0.0022	-0.2459	-0.2964	-0.2557	0.4002	-0.0208	0.2161	-0.0068	-0.0234	0.414	0.0295	0.3894	-19.7179	5.9318	12.1959
2	0.3495	0.2324	-0.2132	0.1969	-0.2182	0.2849	0.0374	-0.0939	-0.1	-0.0922	0.041	0.0112	-0.0119	0.0919	-0	0.287	-0.0326	-0.0139	0.3011	0.0029	0.2888	-34.7774	8.3076	-0.532
3	0.1133	0.0988	-0.0386	0.0736	-0.0057	0.0605	0.0935	-0.0566	-0.298	0.2392	-0.0696	0.0994	0.0693	-0.1176	-0.0005	0.3701	-0.1069	-0.0209	0.3014	0.0398	0.3071	-46.4561	1.2922	2.0278
4	0.0247	-0.0066	0.0366	0.0802	0.0289	0.0638	-0.3234	0.1288	-0.0663	-0.6049	0.1936	0.0846	0.0156	0.0418	-0.0013	0.4658	-0.155	-0.0084	0.3882	0.0134	0.3235	-46.5998	0.9007	-13.903
5	0.0488	-0.0714	-0.0282	0.2202	0.0117	0.044	-0.049	0.2821	0.1328	-0.3171	0.0273	-0.0854	-0.2161	0.263	0.0001	0.2945	-0.0819	0.0852	0.3532	-0.0507	0.3369	-26.0823	9.2073	-5.4324
6	0.1648	-0.2389	0.0785	0.3954	-0.2924	0.4449	0.0615	0.0114	-0.1879	0.0134	-0.0537	-0.0111	0.3488	0.1242	0.0001	0.3452	-0.0419	0.0641	0.4794	-0.0563	0.4806	-19.0531	-4.609	-4.6772
7	0.2633	0.1809	0.0571	0.2894	0.1551	0.0762	0.0177	0.232	-0.2965	-0.1133	0.0796	-0.0513	0.1674	0.3523	0.0004	0.3603	0.0182	0.0256	0.4505	-0.0811	0.4811	-22.1145	-9.8712	-0.8459
8	0.2825	0.0746	-0.0271	0.0793	0.0112	0.2808	-0.1101	0.1606	-0.1444	0.0468	-0.1637	-0.2991	0.1892	0.1531	-0.2197	0.1981	0.081	-0.0135	0.4514	-0.0175	0.3906	-15.0451	-9.3428	5.2194
9	0.041	0.0572	-0.0294	0.0286	-0.0274	0.0341	0.0092	0.0818	-0.0168	0.0059	-0.1589	0.0206	0.2492	-0.1891	-0.0003	0.4783	-0.1829	0.017	0.4474	-0.0837	0.4456	-36.1583	-12.9526	13.9267
10	0.1186	0.0828	-0.0945	0.1016	0.0495	0.2039	-0.2224	0.0658	0.0427	0.175	0.2308	0.0054	-0.2732	0.1637	-0	0.3506	0.0033	0.0067	0.3942	-0.026	0.2693	-26.7149	13.2222	17.524
11	0.3621	0.1205	-0.2582	0.3669	0.2392	0.4432	-0.1794	-0.183	0.0021	0.1425	0.3322	-0.3216	0.0851	-0.088	0.0061	0.3665	0.0323	-0.0569	0.2781	0.0045	0.2712	-27.4963	-2.72	29.2147
12	0.0506	0.0605	0.0464	0.0714	0.0468	0.0403	-0.0202	-0.0988	0.1935	0.033	0.1573	0.1949	0.1599	-0.1407	0.0006	0.6299	-0.0779	0.0106	0.4337	0.0938	0.3449	-37.9631	-12.6669	26.7039
13	0.8689	-0.8656	-0.0769	1.2223	-0.1124	0.1016	-0.0468	-0.4112	0.0333	0.3744	0.1215	-0.3497	0.4394	-0.0264	0.051	0.8624	-0.0752	0.0157	0.5476	0.1132	0.2427	-32.5916	-10.3408	40.9476
14	0.0973	0.019	0.1947	0.1891	0.2316	0.6092	-0	-0.0734	0.1172	0.1327	0.1443	0.023	0.0345	-0.1028	0	0.299	0.0108	0.0052	0.3013	-0.0415	0.2755	-30.1956	16.9561	32.3259
15	0.0139	0.0186	-0.0119	0.0166	-0.0117	0.0068	-0.1779	0.2396	0.2806	0.2263	0.1155	-0.0113	0.1323	-0.3906	-0.0003	0.6208	-0.2531	0.066	0.8504	0.0055	0.6112	-47.5965	6.4497	35.1369
16	0.1222	-0.1509	-0.1155	0.2919	0.2226	0.1555	-0.0027	-0.1195	0.0189	0.146	0.0178	0.2149	0.0194	-0.0722	-0	0.2376	-0.0354	0.0446	0.3643	-0.0052	0.2822	-42.9943	13.1547	29.2096
17	0.1349	0.0274	0.0034	0.078	-0.1617	0.3619	0.0231	-0.0724	0.0204	-0.1346	-0.0973	-0.1743	0.0213	-0.3573	0.0008	0.332	0.0097	0.0221	0.3155	-0.0194	0.2308	-40.5127	15.4505	22.2597
18	0.0786	0.0004	-0.0214	-0.0022	-0.0018	0.0096	0.0541	0.0993	0.3781	0.0739	-0.0816	0.4056	0.2072	-0.3667	-0.0006	0.385	-0.191	0.0607	0.5225	0.0297	0.4808	-53.0899	-0.5764	6.0645
19	0.057	-0.0295	0.1087	0.074	-0.2319	0.386	0.0201	-0.1615	-0.1061	-0.0792	-0.0404	-0.2081	0.181	0.0394	-0.0732	0.1807	0.001	0.0463	0.3665	-0.0464	0.3742	-29.7699	41.6392	66.227
20	0.4489	-0.3438	-0.3001	0.9009	0.4878	1.4925	0.2186	0.2203	0.0785	-0.2438	0.1188	-0.2798	-0.2783	0.0183	0.4619	0.2791	-0.0255	0.1462	0.227	0.0086	0.2661	-34.9762	50.0719	45.618
21	0.1076	-0.0147	-0.0226	0.4156	-0.1716	0.3589	0.0443	0.1085	0.041	-0.1251	0.0289	-0.0303	-0.1091	-0.3009	0.0027	0.2588	0.0346	-0.0386	0.3266	0.0153	0.2414	-52.8075	42.2716	54.8211
22	0.137	0.0986	-0.2575	0.0674	-0.1822	0.7776	0.015	-0.1009	-0.0042	-0.1065	-0.28	-0.4745	0.2512	0.2357	-0.1106	0.2656	-0.0377	-0.0024	0.3062	-0.0314	0.484	-31.5705	46.8879	69.5599
23	0.2085	-0.2513	-0.1068	0.273	0.0863	0.1323	0.0235	-0.005	0.1267	0.1478	0.0665	-0.0404	0.0466	0.0699	0	0.3205	0.0377	-0.0184	0.277	0.0107	0.3008	-50.3616	44.76	75.0839
24	0.0901	-0.0796	0.0345	0.0641	-0.0461	0.0522	-0.0105	0.2489	0.3149	-0.2438	0.0078	0.1964	0.0999	-0.2821	-0.0011	0.3412	0.0774	0.01	0.3936	0.0659	0.3868	-59.9872	51.851	68.0341
25	0.0451	-0.0341	0.005	0.0276	-0.0004	0.0067	-0.208	-0.3548	0.0214	0.3751	0.2117	0.1228	-0.1362	-0.0454	-0	0.4734	0.1036	0.1396	0.4437	0.0816	0.4242	-66.5375	52.3034	82.4857
26	0.0548	0.0656	0.0609	0.6952	0.3206	0.1647	-0.1345	-0.3645	-0.241	0.6201	0.0424	-0.1802	0.2512	0.0871	0.0678	0.4065	0.1024	-0.1439	0.3141	-0.0137	0.305	-44.4652	43.8095	83.1011
27	0.6064	0.528	-0.6399	0.6088	-0.4046	1.5638	0.1203	-0.2204	0.1975	0.4652	0.0111	-0.1886	-0.468	-0.1052	0.2841	0.4458	0.039	-0.1962	0.4138	-0.0793	0.4314	-38.5915	57.9744	86.4923
28	0.1638	0.099	-0.1862	0.5154	0.7064	1.7176	0.1111	-0.0004	0.2761	-0.2158	0.1266	-0.6919	-0.6967	-0.0642	0.3797	0.1715	-0.0844	-0.0716	0.2642	-0.1337	0.5667	-31.7873	64.0984	74.8473
29	0.0093	-0.008	0.0122	-0.0071	-0.0144	0.0121	0.1595	-0.2181	-0.1131	-0.1457	-0.0469	-0.1448	-0.157	-0.3628	0.0005	0.4932	0.1366	0.0236	0.4106	-0.0211	0.4713	-45.5374	65.9287	61.2376

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 51:79 )
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 80:151 )
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 152:169 )
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 170:187 )
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 188:217 )
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 218:278 )
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 279:311 )
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 312:344 )
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 345:367 )
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 52:79 )
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 80:151 )
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 152:172 )
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 173:199 )
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 200:259 )
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 260:278 )
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 279:311 )
17	X-RAY DIFFRACTION	17	(CHAIN B AND RESID 312:354 )
18	X-RAY DIFFRACTION	18	(CHAIN B AND RESID 355:372 )
19	X-RAY DIFFRACTION	19	(CHAIN C AND RESID 44:79 )
20	X-RAY DIFFRACTION	20	(CHAIN C AND RESID 80:296 )
21	X-RAY DIFFRACTION	21	(CHAIN C AND RESID 297:372 )
22	X-RAY DIFFRACTION	22	(CHAIN D AND RESID 51:79 )
23	X-RAY DIFFRACTION	23	(CHAIN D AND RESID 80:151 )
24	X-RAY DIFFRACTION	24	(CHAIN D AND RESID 152:169 )
25	X-RAY DIFFRACTION	25	(CHAIN D AND RESID 170:187 )
26	X-RAY DIFFRACTION	26	(CHAIN D AND RESID 188:217 )
27	X-RAY DIFFRACTION	27	(CHAIN D AND RESID 218:296 )
28	X-RAY DIFFRACTION	28	(CHAIN D AND RESID 297:344 )
29	X-RAY DIFFRACTION	29	(CHAIN D AND RESID 345:367 )

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