PDB-2x06: SULFOLACTATE DEHYDROGENASE FROM METHANOCALDOCOCCUS JANNASCHII

ID or keywords:

Entry

Database: PDB / ID: 2x06

Title

SULFOLACTATE DEHYDROGENASE FROM METHANOCALDOCOCCUS JANNASCHII

Components

L-SULFOLACTATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / HYPERTHERMOSTABLE /

COENZYME M /

METHANOGENS / COENZYME M BIOSYNTHESIS / PRO-S HYDROGEN TRANSFER / NAD-BINDING WITHOUT A ROSSMANN FOLD

Function / homology

Function and homology information

L-2-hydroxycarboxylate dehydrogenase (NAD+) / coenzyme M biosynthetic process /

L-2-hydroxycarboxylate dehydrogenase (NAD+) activity /

sulfopyruvate decarboxylase activity /

cytoplasm
Similarity search - Function

Biological species

METHANOCALDOCOCCUS JANNASCHII (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.5 Å

Authors

Irimia, A. / Madern, D. / Zaccai, G. / Vellieux, F.M.D.

Citation

Journal: Embo J. / Year: 2004
Title: Methanoarchaeal Sulfolactate Dehydrogenase: Prototype of a New Family of Nadh-Dependent Enzymes.
Authors: Irimia, A. / Madern, D. / Vellieux, F.M.D.

History

Deposition	Dec 7, 2009	Deposition site: PDBE / Processing site: PDBE
Supersession	Dec 15, 2009	ID: 1RFM
Revision 1.0	Dec 15, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jul 5, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Jan 30, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5	Feb 6, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2x06.cif.gz	1 MB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2x06.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/2x06 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/2x06	HTTPS FTP

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Related structure data

Similar structure data	1x0a-1 5aq5-4 3uoe-d 2g8y-d 3i0p-1 5n4a-d 30051 4uw7-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: L-SULFOLACTATE DEHYDROGENASE

B: L-SULFOLACTATE DEHYDROGENASE

C: L-SULFOLACTATE DEHYDROGENASE

D: L-SULFOLACTATE DEHYDROGENASE

E: L-SULFOLACTATE DEHYDROGENASE

F: L-SULFOLACTATE DEHYDROGENASE

G: L-SULFOLACTATE DEHYDROGENASE

H: L-SULFOLACTATE DEHYDROGENASE

hetero molecules

308 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

G: L-SULFOLACTATE DEHYDROGENASE

H: L-SULFOLACTATE DEHYDROGENASE

hetero molecules

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

2

E: L-SULFOLACTATE DEHYDROGENASE

F: L-SULFOLACTATE DEHYDROGENASE

hetero molecules

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

3

C: L-SULFOLACTATE DEHYDROGENASE

D: L-SULFOLACTATE DEHYDROGENASE

hetero molecules

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

4

A: L-SULFOLACTATE DEHYDROGENASE

B: L-SULFOLACTATE DEHYDROGENASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.930, 203.710, 100.050
Angle α, β, γ (deg.)	90.00, 112.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	L-SULFOLACTATE DEHYDROGENASE / (R)-SULFOLACTATE DEHYDROGENASE / (R)-2-HYDROXYACID DEHYDROGENASE Mass: 37831.434 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea) Plasmid: PT 77 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58820, EC: 1.1.1.272
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.41 % / Description: NONE
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: PEG 8000, SODIUM CHLORIDE, NADH, SPERMINE TETRA-HCL, TRIS, PH 7.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: BM30A / Wavelength: 0.979682, 0.979558, 0.977769

Detector

Type: MARRESEARCH / Detector: CCD / Date: Dec 7, 2002 / Details: MIRRORS

Radiation

Monochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979682	1
2	0.979558	1
3	0.977769	1

Reflection

Resolution: 2.5→101.86 Å / Num. obs: 2309530 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 23.26 % / B_iso Wilson estimate: 31.38 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 22.14

Reflection shell

Resolution: 2.5→2.67 Å / Redundancy: 12.34 % / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 3.62 / % possible all: 84.6

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Processing

Software

Name	Classification
XDS	data reduction
XSCALE	data scaling
TRUNCATE	data scaling
SnB	phasing
MLPHARE	phasing
PHENIX	refinement

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.5→32.831 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 21.29 / Stereochemistry target values: ML / Details: RE-REFINEMENT OF PDB ENTRY 1RFM USING PHENIX

	R_factor	Num. reflection	% reflection
R_free	0.2242	4958	5 %
R_work	0.153	-	-
obs	0.1567	99250	96.06 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.892 Å² / k_sol: 0.345 e/Å³

Displacement parameters

B_iso mean: 38.43 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.3254 Å²	-0 Å²	3.282 Å²
2-	-	5.5172 Å²	-0 Å²
3-	-	-	-0.1918 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→32.831 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20984	0	352	500	21836

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	21745
X-RAY DIFFRACTION	f_angle_d	1.326	29298
X-RAY DIFFRACTION	f_dihedral_angle_d	20.04	8733
X-RAY DIFFRACTION	f_chiral_restr	0.115	3287
X-RAY DIFFRACTION	f_plane_restr	0.005	3771

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 (%)
2.5001-2.5895	0.4109	374	0.3118	7233	X-RAY DIFFRACTION	74
2.5895-2.6931	0.2799	508	0.189	9648	X-RAY DIFFRACTION	98
2.6931-2.8156	0.2554	448	0.1774	9632	X-RAY DIFFRACTION	98
2.8156-2.964	0.2692	497	0.1775	9632	X-RAY DIFFRACTION	98
2.964-3.1495	0.2446	523	0.1696	9602	X-RAY DIFFRACTION	98
3.1495-3.3925	0.2434	540	0.1541	9662	X-RAY DIFFRACTION	99
3.3925-3.7334	0.2	506	0.1285	9669	X-RAY DIFFRACTION	99
3.7334-4.2727	0.185	514	0.1152	9730	X-RAY DIFFRACTION	99
4.2727-5.3793	0.1748	539	0.1107	9724	X-RAY DIFFRACTION	99
5.3793-32.8337	0.1945	509	0.1425	9760	X-RAY DIFFRACTION	99

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	1.1875	0.3959	-0.2404	-0.1986	0.4092	0.661	-0.0051	-0.0919	-0.0678	-0.0403	0.0304	0.0504	-0.0549	-0.1087	0.0217	0.0823	0.0129	-0.0453	0.0801	-0.0438	0.085	-9.7458	195.1668	20.7769
2	0.2146	0.002	-0.3336	0.3674	0.0421	0.4509	-0.1029	-0.0671	-0.1741	0.3752	0.0801	0.0214	-0.5253	-0.3003	0.2101	0.2626	0.1422	-0.0756	0.2189	0.0116	0.3184	-15.2486	217.6087	6.9671
3	0.6462	0.2434	-0.2903	0.2804	0.0652	0.1623	-0.0135	0.2409	-0.0844	-0.0016	-0.0737	0.0748	0.0931	-0.009	0.0472	0.0914	-0.0132	-0.0411	0.1518	-0.0678	0.1304	-2.1096	197.8171	11.6555
4	0.5258	0.1078	-0.5031	0.8501	-0.0237	0.5149	0.1115	-0.1959	0.1598	0.1058	-0.0188	0.0712	-0.1081	-0.1247	-0.0234	0.1189	0.0191	-0.0336	0.0927	-0.0522	0.0224	-12.4807	207.5545	30.1157
5	0.6127	0.2645	-0.1069	0.0734	-0.0813	0.4063	-0.0182	0.0097	-0.1014	0.0588	0.0329	-0.1273	0.0183	-0.017	-0.013	0.0487	-0.0164	-0.027	0.0392	-0.0109	0.1155	27.1474	203.6838	12.9929
6	0.6081	0.3069	0.0747	0.204	0.5484	0.4371	-0.0692	0.1123	0.3498	0.1035	-0.0546	0.1131	-0.0312	0.0376	0.157	0.1687	-0.0049	-0.0617	0.0834	0.0271	0.1436	11.3544	217.9871	12.6737
7	0.3064	0.113	0.3419	0.5173	0.1298	0.2863	-0.0116	-0.1824	0.1883	0.0584	-0.1326	0.1743	-0.0408	0.0068	0.1028	0.0881	-0.0043	-0.0182	0.0929	0.0033	0.1717	13.8499	218.0069	23.1279
8	0.8271	-0.307	0.0495	0.1509	0.2044	0.3155	-0.0651	0.2811	0.1527	-0.1792	0.0253	0.018	0.0236	-0.0299	0.0149	0.1831	-0.0275	-0.0451	0.1172	0.0191	0.0532	18.5911	208.0671	0.6096
9	0.7376	0.5594	0.1222	2.1197	-0.8701	1.6554	-0.1581	0.1318	0.2484	-0.0541	-0.4303	-0.6998	-0.0861	0.484	0.3674	0.0734	-0.0483	-0.0823	0.2033	0.1176	0.2382	21.4487	192.7922	49.46
10	0.7976	0.2976	-0.1136	0.2779	-0.4255	0.2802	-0.0474	-0.0232	-0.0492	-0.0118	0.0188	-0.0281	-0.0841	0.1207	-0.0264	0.0747	0.0298	-0.0493	0.0709	-0.0443	0.0708	4.4611	185.2009	53.3124
11	0.3901	-0.0101	-0.2223	0.4302	-0.3367	0.8295	-0.0124	-0.1634	0.0758	0.1436	-0.0005	-0.2627	-0.3002	0.2033	-0.0337	0.1348	-0.0578	-0.084	0.1863	-0.0506	0.1415	5.7309	195.0037	65.6347
12	1.4595	-0.1695	-0.3082	0.8054	-1.1451	1.0319	0.1186	0.183	0.3496	0.3988	-0.2721	-0.18	-0.3702	0.2504	0.152	0.1937	-0.094	-0.1375	0.0604	-0.033	0.051	8.6253	204.0488	48.6748
13	0.2553	0.2501	-0.0696	1.1406	0.5102	0.5705	0.102	-0.1264	-0.1225	-0.0716	0.1811	-0.3296	0.3969	0.0258	-0.182	0.1403	-0.0336	0.0053	0.3372	-0.0233	0.0778	-38.1851	184.0201	68.7648
14	0.5329	-0.0746	-0.309	-0.1313	-0.2244	0.8604	-0.0259	-0.0364	0.0321	0.0739	-0.0522	0.0734	-0.0413	-0.0904	0.0438	0.1045	0.0225	-0.0259	0.1347	-0.0761	0.0608	-21.9177	188.1481	59.2571
15	0.4601	-0.2793	-0.1991	0.12	-0.0273	0.1722	0.0257	-0.0735	-0.0283	-0.1425	-0.0405	-0.0175	-0.1905	-0.1776	0.0803	0.1834	0.0531	-0.0263	0.1951	-0.0864	0.0567	-18.3729	205.7547	63.3649
16	2.0433	0.1415	0.3478	0.5295	0.063	0.8076	-0.0938	-0.7027	-0.1151	0.1222	0.0454	0.0488	0.0553	-0.1774	-0.0134	0.211	0.0474	-0.0524	0.2921	-0.0178	0.0153	-19.4997	184.9757	73.4457
17	0.4401	-0.3937	0.3007	0.5836	0.0842	0.304	0.1997	0.2033	-0.2137	-0.0923	-0.1953	-0.1082	-0.0034	0.15	0.0659	0.1005	-0.0349	-0.0174	0.2481	-0.0584	0.1551	-18.9256	151.6556	19.8983
18	0.3071	-0.3321	0.2472	0.5742	-0.1363	0.1343	-0.0408	0.0421	0.1527	-0.1525	0.052	0.088	0.0031	-0.0678	0.0205	0.1113	-0.0459	0.0029	0.0757	-0.0528	0.1273	-10.2915	153.6071	36.3778
19	0.6775	0.0302	0.1074	0.2389	0.2662	0.1451	0.0445	-0.1923	0.1216	-0.1297	-0.0692	0.0364	0.0346	-0.014	-0.0332	0.2346	-0.0099	-0.0261	0.1561	0.0032	0.2146	-22.1096	133.4526	40.0956
20	0.2248	-0.0339	0.5451	-0.0835	-0.0562	0.9741	0.0505	0.0628	-0.1124	-0.0104	0.0141	0.0271	0.1028	0.1042	-0.0481	0.1209	-0.0127	0.0032	0.0643	-0.0622	0.1926	-10.0926	144.5614	27.9921
21	0.4517	-0.3804	0.0152	0.2871	-0.4738	0.618	-0.0941	0.0194	-0.1415	0.1905	0.0653	-0.1045	0.0316	0.0603	0.0405	0.1581	0.0372	-0.016	0.029	0.0263	0.1363	5.832	143.125	59.4946
22	0.8608	-0.0981	-1.169	0.0699	0.0514	1.576	-0.2092	-0.4076	-0.359	0.6541	-0.2383	-0.0889	0.2639	0.5371	0.1614	0.4897	-0.0006	0.1017	0.1322	0.1149	0.409	-1.0147	121.3625	48.2024
23	0.3363	0.0279	0.3255	0.3871	0.0309	0.9993	0.0331	-0.0927	-0.0609	0.2199	-0.0517	-0.0217	0.1391	-0.0169	0.0211	0.1442	-0.0149	0.046	0.0026	0.0314	0.085	-5.3678	144.3741	52.6788
24	1.8232	-0.2763	0.0674	0.3609	-0.1117	1.1485	-0.28	-0.6746	-0.3783	0.2462	0.243	-0.038	0.2975	-0.2048	0.0115	0.2641	0.0242	0.0228	0.1212	0.089	0.2347	4.5034	131.9296	76.2163
25	0.8771	0.2417	-0.2129	0.6961	-0.3163	0.4693	0.0273	-0.1361	-0.0834	0.0134	-0.0962	-0.0245	-0.064	0.0282	0.0485	0.0809	0.0034	-0.0133	0.1161	-0.0195	0.1084	23.3505	161.1134	26.7717
26	0.2965	-0.2715	-0.0187	0.5633	0.2687	0.1913	0.0191	-0.0636	0.1141	-0.0324	0.0036	-0.1777	0.2234	0.171	-0.022	0.1696	0.0747	0.0153	0.1225	-0.0114	0.176	26.7462	150.3661	9.5982
27	0.5467	0.5066	0.2108	0.3591	0.1238	0.6844	0.0376	0.0921	-0.0056	0.0722	-0.0687	-0.1829	0.1067	0.1494	-0.0197	0.1051	0.012	-0.0246	0.0939	-0.0614	0.1347	19.8476	154.4798	9.8144
28	0.3901	-0.3571	0.1684	0.3866	0.2921	1.9504	0.0548	0.005	-0.3226	0.1026	0.0359	-0.2061	0.4564	0.4002	0.0067	0.1484	0.0346	-0.0015	0.1437	0.0404	0.2576	29.4757	144.5442	30.3884
29	0.312	-0.1268	0.148	0.123	0.026	0.2197	0.0234	0.0055	0.0449	-0.091	-0.0739	0.0169	-0.0224	-0.1598	0.0089	0.0938	-0.0248	-0.0067	0.1991	-0.0861	0.0896	0.6067	162.3258	-9.844
30	0.0439	-0.008	-0.4472	0.2733	0.0644	0.5583	-0.1274	0.2473	-0.037	-0.0047	0.0658	0.1954	0.2562	-0.1376	0.1098	0.1927	-0.044	0.0555	0.0983	-0.1081	0.0741	15.1009	144.5251	-5.9265
31	0.155	0.0154	-0.0327	0.3411	0.2661	0.1543	-0.0708	-0.0168	0.2055	-0.0781	-0.2198	0.2104	0.091	-0.2783	0.1256	0.2426	-0.0703	-0.0128	0.1817	-0.0979	0.2122	1.7617	147.9421	1.1649
32	1.0894	0.0507	0.4398	0.2331	0.2221	1.452	0.1538	0.358	0.0594	-0.0967	-0.1046	-0.0246	0.0219	0.1317	-0.1027	0.1986	0.0313	0.0203	0.2019	-0.0845	0.1067	14.2801	161.8452	-13.01

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:176)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 177:220)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 221:273)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 274:344)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 1:139)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 140:200)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 201:262)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 263:344)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 1:64)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 65:162)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 163:270)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 271:344)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 1:26)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 27:173)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 174:262)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 263:344)
17	X-RAY DIFFRACTION	17	(CHAIN E AND RESID 1:57)
18	X-RAY DIFFRACTION	18	(CHAIN E AND RESID 58:172)
19	X-RAY DIFFRACTION	19	(CHAIN E AND RESID 173:236)
20	X-RAY DIFFRACTION	20	(CHAIN E AND RESID 237:344)
21	X-RAY DIFFRACTION	21	(CHAIN F AND RESID 1:179)
22	X-RAY DIFFRACTION	22	(CHAIN F AND RESID 180:232)
23	X-RAY DIFFRACTION	23	(CHAIN F AND RESID 233:306)
24	X-RAY DIFFRACTION	24	(CHAIN F AND RESID 307:344)
25	X-RAY DIFFRACTION	25	(CHAIN G AND RESID 1:127)
26	X-RAY DIFFRACTION	26	(CHAIN G AND RESID 128:206)
27	X-RAY DIFFRACTION	27	(CHAIN G AND RESID 207:297)
28	X-RAY DIFFRACTION	28	(CHAIN G AND RESID 298:344)
29	X-RAY DIFFRACTION	29	(CHAIN H AND RESID 1:135)
30	X-RAY DIFFRACTION	30	(CHAIN H AND RESID 136:227)
31	X-RAY DIFFRACTION	31	(CHAIN H AND RESID 228:255)
32	X-RAY DIFFRACTION	32	(CHAIN H AND RESID 256:344)

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