PDB-4bgv: 1.8 A resolution structure of the malate dehydrogenase from Picro...

ID or keywords:

Entry

Database: PDB / ID: 4bgv

Title

1.8 A resolution structure of the malate dehydrogenase from Picrophilus torridus in its apo form

Components

MALATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / HYPERACIDOPHILE / TRICARBOXYLIC ACID CYCLE

Function / homology

Function and homology information

malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / tricarboxylic acid cycle
Similarity search - Function

Biological species

PICROPHILUS TORRIDUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.811 Å

Authors

Talon, R. / Madern, D. / Girard, E.

Citation

Journal: To be Published
Title: Insight Into Structural Evolution of Extremophilic Proteins
Authors: Talon, R. / Girard, E. / Franzetti, B. / Madern, D.

History

Deposition	Mar 28, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2015	Group: Database references
Revision 1.2	Apr 1, 2015	Group: Data collection
Revision 1.3	Mar 6, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4bgv.cif.gz	522.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4bgv_validation.pdf.gz	842.7 KB	Display	wwPDB validaton report
Full document	4bgv_full_validation.pdf.gz	856.1 KB	Display
Data in XML	4bgv_validation.xml.gz	59.6 KB	Display
Data in CIF	4bgv_validation.cif.gz	88.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgv ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgv	HTTPS FTP

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Related structure data

Related structure data	4bguC 4cl3 C: citing same article (ref.)
Similar structure data	4q3n-1 6p6u-1 4qo8-d 6ldh-1 5ulv-1 6vdj-1 3pqf-d 4qo7-d 3vph-d 3hka-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (7) #154 - Oct 2012 Citric Acid Cycle similarity (7) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #142 - Oct 2011 PDB Pioneers similarity (6)

Deposited unit

A: MALATE DEHYDROGENASE

B: MALATE DEHYDROGENASE

C: MALATE DEHYDROGENASE

D: MALATE DEHYDROGENASE

hetero molecules

142 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)	81.167, 81.167, 395.990
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-2088- HOH
2	1	B-2302- HOH
3	1	C-2303- HOH

#1: Protein	MALATE DEHYDROGENASE Mass: 35125.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PICROPHILUS TORRIDUS (archaea) Description: COMPLETE GENE WAS SYNTHESIZED BY GENECUST EUROPE COMPANY Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6L0C3, malate dehydrogenase
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Chemical	ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₆
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1219 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	DUE TO THE PROTEIN PRODUCTION PROTOCOL, EACH MONOMER WERE FOUND DELETED OF THEIR N-TERMINAL METHIONINE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46 % Description: AVERAGE RPIM VALUE IS 3.6 FOR THE DATA SET, 21.1 FOR THE HIGHEST RESOLUTION SHELL
Crystal grow	Temperature: 293 K / pH: 3.5 Details: 9-14 % PEG 4000, 0.1 M CITRIC ACID PH 3.5, 293 K, 12-15 DAYS

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2010 / Details: TWO MIRRORS
Radiation	Monochromator: DOUBLE CRYSTALS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.81→46.47 Å / Num. obs: 121716 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / B_iso Wilson estimate: 15.43 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 6.3
Reflection shell	Resolution: 1.81→1.91 Å / Redundancy: 10.8 % / R_merge(I) obs: 0.67 / Mean I/σ(I) obs: 1.3 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
XDS		data reduction
SCALA		data scaling
PHASER	2.1.4	phasing
PHENIX		refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: ONE POLY-ALA MONOMER OF OUR PREVIOUS SIRAS PTMALDH MODEL

Resolution: 1.811→46.473 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 15.62 / Stereochemistry target values: ML
Details: THE PROTEIN WERE FOUND IN ITS NATIVE HOMOTETRAMERIC STATE INSIDE THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT.

	R_factor	Num. reflection	% reflection
R_free	0.1848	6078	5 %
R_work	0.1464	-	-
obs	0.1483	121529	99.78 %

Solvent computation

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

Displacement parameters

B_iso mean: 17.95 Å²

Refinement step

Cycle: LAST / Resolution: 1.811→46.473 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9880	0	100	1219	11199

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10333
X-RAY DIFFRACTION	f_angle_d	1.096	13960
X-RAY DIFFRACTION	f_dihedral_angle_d	13.003	3930
X-RAY DIFFRACTION	f_chiral_restr	0.077	1581
X-RAY DIFFRACTION	f_plane_restr	0.005	1788

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 (%)
1.8114-1.832	0.2578	187	0.2447	3547	X-RAY DIFFRACTION	93
1.832-1.8536	0.2509	202	0.1806	3838	X-RAY DIFFRACTION	100
1.8536-1.8762	0.2122	197	0.1695	3756	X-RAY DIFFRACTION	100
1.8762-1.8999	0.2098	200	0.162	3783	X-RAY DIFFRACTION	100
1.8999-1.9249	0.2099	199	0.162	3795	X-RAY DIFFRACTION	100
1.9249-1.9513	0.1884	201	0.1548	3803	X-RAY DIFFRACTION	100
1.9513-1.9792	0.2121	201	0.1563	3832	X-RAY DIFFRACTION	100
1.9792-2.0087	0.2024	198	0.1575	3754	X-RAY DIFFRACTION	100
2.0087-2.0401	0.2051	201	0.1491	3813	X-RAY DIFFRACTION	100
2.0401-2.0736	0.2196	199	0.1436	3794	X-RAY DIFFRACTION	100
2.0736-2.1093	0.1825	200	0.1414	3786	X-RAY DIFFRACTION	100
2.1093-2.1477	0.1892	201	0.1342	3830	X-RAY DIFFRACTION	100
2.1477-2.189	0.187	201	0.1387	3830	X-RAY DIFFRACTION	100
2.189-2.2337	0.1935	200	0.1336	3802	X-RAY DIFFRACTION	100
2.2337-2.2822	0.166	202	0.1334	3813	X-RAY DIFFRACTION	100
2.2822-2.3353	0.1823	202	0.1411	3851	X-RAY DIFFRACTION	100
2.3353-2.3937	0.1737	202	0.1397	3840	X-RAY DIFFRACTION	100
2.3937-2.4584	0.192	202	0.1378	3829	X-RAY DIFFRACTION	100
2.4584-2.5308	0.195	200	0.1456	3819	X-RAY DIFFRACTION	100
2.5308-2.6125	0.1861	205	0.146	3875	X-RAY DIFFRACTION	100
2.6125-2.7058	0.1794	202	0.1405	3854	X-RAY DIFFRACTION	100
2.7058-2.8141	0.1639	202	0.1388	3839	X-RAY DIFFRACTION	100
2.8141-2.9422	0.184	203	0.1449	3857	X-RAY DIFFRACTION	100
2.9422-3.0973	0.2017	204	0.1522	3884	X-RAY DIFFRACTION	100
3.0973-3.2913	0.1743	206	0.1407	3895	X-RAY DIFFRACTION	100
3.2913-3.5453	0.163	207	0.143	3919	X-RAY DIFFRACTION	100
3.5453-3.902	0.1707	206	0.1401	3930	X-RAY DIFFRACTION	100
3.902-4.4662	0.1471	209	0.1225	3964	X-RAY DIFFRACTION	100
4.4662-5.6254	0.1584	212	0.1364	4027	X-RAY DIFFRACTION	100
5.6254-46.4888	0.2165	227	0.1831	4292	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	1.9409	-0.2944	-0.0864	0.7382	0.022	0.9525	0.0652	0.1394	-0.0411	-0.1287	-0.0244	0.0461	0.0098	-0.0333	-0.0475	0.1076	0.0158	0.0062	0.0556	-0.0092	0.0711	72.3809	44.2163	10.0594
2	2.6309	0.2962	0.0705	2.0972	-0.0415	3.0364	-0.0054	0.3264	0.2259	-0.2049	0.0053	-0.0021	-0.1852	-0.0961	-0.0414	0.1142	0.0189	0.0066	0.1032	0.0105	0.1154	60.706	47.3353	9.0591
3	8.6759	0.2955	2.3095	7.0809	2.7069	9.7858	0.1379	0.6781	1.438	-0.4532	-0.0715	-0.8446	-1.4914	0.8985	-0.0034	0.525	0.1009	0.1129	0.3749	0.1774	0.5783	58.0865	69.756	12.1662
4	0.9	0.1142	0.4647	0.3212	0.269	1.0665	-0.0016	-0.023	0.0765	-0.0321	-0.0097	0.0334	-0.1587	-0.1458	0.0259	0.1212	0.0267	0.025	0.0738	0.0008	0.1102	63.3519	56.0387	27.9955
5	0.5265	0.2482	-0.1115	0.5364	0.1522	0.6948	0.0329	0.0381	0.1635	0.0146	0.0419	0.0953	-0.1408	-0.0107	-0.0378	0.1085	0.0166	0.0211	0.0543	0.0028	0.0931	71.6306	60.7918	25.3266
6	1.0457	-0.4793	-0.384	1.584	0.6853	1.1197	0.0045	-0.076	0.0677	0.0619	0.0021	0.159	-0.1163	-0.2142	0.0309	0.1171	0.0401	0.0352	0.1257	-0.0048	0.114	54.2144	54.1468	33.9603
7	4.255	-1.1548	0.7624	3.0664	-0.3601	5.7462	-0.0405	0.3866	0.2498	-0.2047	-0.1434	0.2281	-0.4519	-0.3342	0.2454	0.2282	0.1653	0.0053	0.2806	0.0379	0.229	46.4611	63.2861	16.7777
8	1.1666	0.0271	-0.4905	1.0773	-0.1658	1.1579	0.0861	-0.0165	0.1092	0.0651	-0.0528	-0.0243	-0.149	0.0626	-0.0073	0.1006	-0.0022	0.0179	0.0477	-0.0053	0.0903	86.5622	58.3569	22.2465
9	2.5958	-0.3088	-0.0262	3.9222	0.4799	2.3659	-0.0015	-0.0306	0.2685	0.1361	0.0104	-0.0215	-0.2541	0.0163	0.0573	0.1112	-0.0206	0.0379	0.0593	-0.0049	0.1398	96.1638	62.142	16.3059
10	7.8745	-1.8121	-0.4881	6.6294	0.1948	5.6321	-0.1436	-0.1839	0.2275	0.2119	-0.0161	0.3332	-0.2961	-0.5374	0.1098	0.782	0.1104	0.1258	0.888	0.1961	0.4987	90.9117	62.3879	-7.1564
11	0.5095	0.3974	0.0657	1.3198	0.4167	0.4037	-0.0163	0.0554	0.0689	-0.2297	0.0353	-0.1055	-0.1327	0.0419	-0.0157	0.133	-0.0066	0.0399	0.0882	0.0058	0.1047	96.7572	46.8602	6.5961
12	1.1095	0.6019	-0.7591	6.4359	-0.7272	1.4311	-0.0515	0.4247	-0.0374	-0.4014	-0.0184	-0.127	-0.0759	-0.0605	0.0682	0.1214	-0.0083	0.0185	0.1822	-0.008	0.0984	87.727	29.9571	-5.9782
13	0.9205	-0.1084	-0.0795	0.7283	0.1504	0.9053	0.0078	0.0274	0.0661	-0.0971	0.0312	-0.1281	-0.0512	0.1208	-0.0217	0.1116	-0.0178	0.0503	0.0525	-0.0103	0.0938	98.3223	44.8395	8.3516
14	0.6355	0.9001	0.2492	5.7154	0.1252	0.5562	0.1208	0.3315	0.1006	-0.5032	0.1775	-0.2564	-0.2375	0.1752	-0.0069	0.2472	-0.0574	0.1846	0.1186	0.0416	0.176	106.3503	49.3791	-4.4476
15	1.0315	0.326	0.0751	1.8706	0.2942	1.213	0.0119	-0.058	-0.0441	0.1079	-0.0099	0.1583	0.0838	-0.0546	-0.0157	0.0799	0.0075	0.0257	0.06	0.0058	0.0772	73.573	25.4889	36.4967
16	2.4195	0.0453	-0.3969	1.7723	-0.167	2.2659	-0.0047	-0.2466	-0.0087	0.3407	0.0062	-0.007	0.2062	-0.18	-0.0394	0.1553	-0.0078	0.0158	0.0756	-0.0098	0.106	70.7338	14.3073	32.7508
17	6.5928	-0.0919	5.2465	4.3127	0.5736	5.3827	-0.0374	-0.5593	-0.3984	0.74	0.0808	-0.801	0.3661	0.4567	-0.071	0.3425	0.0664	-0.0585	0.2622	0.0527	0.2933	87.1439	-0.6054	34.9213
18	1.1788	0.404	-0.4214	0.4893	-0.0585	0.4455	-0.0541	0.0147	-0.1367	0.0028	0.0204	-0.0548	0.0736	0.0118	0.03	0.0961	0.0093	0.0147	0.0578	-0.0023	0.088	87.6527	16.5788	20.4051
19	0.8846	-0.0073	-0.0396	0.2127	0.1197	0.944	-0.044	-0.0877	-0.0834	0.0853	0.0378	-0.0548	0.0936	0.0694	0.0096	0.1112	0.0069	0.0134	0.0493	0.0054	0.0981	93.4999	19.3736	27.8393
20	1.4788	-0.4768	-0.5787	1.2424	0.1686	1.0585	-0.0041	0.1431	-0.1692	-0.0927	-0.05	0.0099	0.0936	-0.0478	0.0419	0.1005	-0.0089	0.0248	0.0724	-0.0124	0.0962	84.8907	12.2714	10.5004
21	5.1246	2.0167	-2.2323	4.285	-1.3782	3.9083	-0.1748	-0.0003	-0.2416	-0.0165	-0.0034	0.0349	0.1344	0.0111	0.1586	0.22	0.0131	0.0448	0.0578	-0.0052	0.1753	80.5831	-3.3941	23.2693
22	1.2405	-0.1756	0.5622	1.1596	0.4862	1.9768	-0.0121	0.0246	-0.017	0.0768	0.0322	-0.0946	0.0266	0.1873	-0.0149	0.0811	-0.0057	0.0142	0.0697	-0.0019	0.0849	96.3623	31.3312	37.1094
23	4.0405	-0.461	0.333	3.7907	0.0936	3.4161	-0.0604	-0.2129	-0.2217	0.2518	0.0108	-0.2751	0.2769	0.113	0.0706	0.1477	0.0024	-0.0093	0.1132	-0.0245	0.109	100.4612	34.5145	47.9538
24	7.023	-4.0475	4.3094	6.1285	-4.0439	8.17	0.0407	0.3696	-0.7617	-1.4132	0.1291	0.5408	1.0757	-0.9954	-0.2282	1.1624	-0.231	-0.0046	0.8599	0.2474	0.52	84.7451	26.6297	65.1933
25	1.4554	-0.2872	0.2562	0.4077	0.1566	0.4565	-0.0592	-0.2461	-0.0024	0.1437	0.0645	-0.0213	0.0016	-0.0038	-0.0158	0.1566	-0.002	0.0109	0.119	0.0113	0.0783	84.0265	41.7229	51.8599
26	6.0889	-4.1841	2.8438	3.5162	-1.7628	3.303	-0.0608	-0.5127	-0.0785	0.3694	0.1612	0.2434	-0.1125	-0.4451	-0.0976	0.1867	-0.0323	0.0705	0.1891	-0.005	0.1379	60.7285	41.0589	52.8457
27	1.0761	-0.123	-0.0769	0.8406	0.2171	0.9537	-0.0134	-0.1968	0.0864	0.1624	0.0476	-0.0656	-0.0693	0.0325	-0.0353	0.1115	0.0187	0.0042	0.1035	-0.0161	0.0519	83.8583	44.5373	50.7263
28	3.1811	-1.2169	0.0163	1.8711	-0.0418	1.167	-0.0431	-0.585	-0.0009	0.4476	0.1343	0.0075	-0.0419	-0.1889	-0.0413	0.2954	0.0624	0.0405	0.3956	-0.0164	0.0701	83.9767	45.2512	66.5582

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:67)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 68:88)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 89:100)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 101:206)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 207:248)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 249:306)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 307:324)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 1:67)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 68:88)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 89:95)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 96:199)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 200:213)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 214:292)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 293:324)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 1:67)
16	X-RAY DIFFRACTION	16	(CHAIN C AND RESID 68:88)
17	X-RAY DIFFRACTION	17	(CHAIN C AND RESID 89:100)
18	X-RAY DIFFRACTION	18	(CHAIN C AND RESID 101:206)
19	X-RAY DIFFRACTION	19	(CHAIN C AND RESID 207:248)
20	X-RAY DIFFRACTION	20	(CHAIN C AND RESID 249:306)
21	X-RAY DIFFRACTION	21	(CHAIN C AND RESID 307:324)
22	X-RAY DIFFRACTION	22	(CHAIN D AND RESID 1:67)
23	X-RAY DIFFRACTION	23	(CHAIN D AND RESID 68:88)
24	X-RAY DIFFRACTION	24	(CHAIN D AND RESID 89:95)
25	X-RAY DIFFRACTION	25	(CHAIN D AND RESID 96:199)
26	X-RAY DIFFRACTION	26	(CHAIN D AND RESID 200:213)
27	X-RAY DIFFRACTION	27	(CHAIN D AND RESID 214:292)
28	X-RAY DIFFRACTION	28	(CHAIN D AND RESID 293:324)

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