PDB-8sc0: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogen...

ID or keywords:

Entry

Database: PDB / ID: 8sc0

Title

Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (NAD bound, orthorhombic form)

Components

2,3-dihydroxybenzoate-2,3-dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID /

STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

Function / homology

Function and homology information

2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase /

2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase activity / siderophore biosynthetic process /

nucleotide binding
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.81 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201700059C	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (NAD bound, orthorhombic form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Apr 4, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sc0.cif.gz	390.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8sc0.ent.gz	321.1 KB	Display	PDB format
PDBx/mmJSON format	8sc0.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/sc/8sc0 ftp://data.pdbj.org/pub/pdb/validation_reports/sc/8sc0	HTTPS FTP

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Related structure data

Similar structure data	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	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: 2,3-dihydroxybenzoate-2,3-dehydrogenase

B: 2,3-dihydroxybenzoate-2,3-dehydrogenase

C: 2,3-dihydroxybenzoate-2,3-dehydrogenase

D: 2,3-dihydroxybenzoate-2,3-dehydrogenase

hetero molecules

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

1

A: 2,3-dihydroxybenzoate-2,3-dehydrogenase

hetero molecules

defined by author
Evidence: gel filtration
27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 2,3-dihydroxybenzoate-2,3-dehydrogenase

hetero molecules

defined by author
27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 2,3-dihydroxybenzoate-2,3-dehydrogenase

hetero molecules

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: 2,3-dihydroxybenzoate-2,3-dehydrogenase

hetero molecules

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.970, 91.942, 144.165
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	2,3-dihydroxybenzoate-2,3-dehydrogenase Mass: 27572.984 Da / Num. of mol.: 4 / Mutation: A2N, A3G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: EAE_13665 / Plasmid: KlaeA.01365.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FXS4
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.12 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: JCSG+ D12: 0.04 M Pottasium Phosphate, 16% PEG 8K, 20% Glycerol. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: 13164, well D12 drop 2, ...Details: JCSG+ D12: 0.04 M Pottasium Phosphate, 16% PEG 8K, 20% Glycerol. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: 13164, well D12 drop 2, Puck: PSL-0615, Cryo: Direct. Subunits C and D contain NAD. Subunits A and B have interlaced alternate conformations from residues 180-196 and were refined with partial occupancies

Crystal

Density Matthews: 2.16 Å³/Da / Density % sol: 43.12 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: JCSG+ D12: 0.04 M Pottasium Phosphate, 16% PEG 8K, 20% Glycerol. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: 13164, well D12 drop 2, ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.8→91.94 Å / Num. obs: 89308 / % possible obs: 100 % / Redundancy: 12.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.035 / R_rim(I) all: 0.127 / Χ²: 1.02 / Net I/σ(I): 13 / Num. measured all: 1145982
Reflection shell	Resolution: 1.8→1.85 Å / % possible obs: 100 % / Redundancy: 12.7 % / R_merge(I) obs: 1.419 / Num. measured all: 82195 / Num. unique obs: 6485 / CC_1/2: 0.765 / R_pim(I) all: 0.412 / R_rim(I) all: 1.478 / Χ²: 1.02 / Net I/σ(I) obs: 2

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_4918: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.81→42.59 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 20.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2051	4315	4.98 %
R_work	0.1693	-	-
obs	0.1711	86711	99.22 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.81→42.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7169	0	112	556	7837

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7741
X-RAY DIFFRACTION	f_angle_d	0.637	10525
X-RAY DIFFRACTION	f_dihedral_angle_d	13.179	2697
X-RAY DIFFRACTION	f_chiral_restr	0.046	1215
X-RAY DIFFRACTION	f_plane_restr	0.006	1383

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 (%)
1.81-1.83	0.0277	122	0.028	2137	X-RAY DIFFRACTION	78
1.83-1.86	0.7047	132	0.6835	2748	X-RAY DIFFRACTION	99
1.86-1.88	0.3546	135	0.27	2735	X-RAY DIFFRACTION	100
1.88-1.9	0.2497	140	0.2184	2722	X-RAY DIFFRACTION	100
1.9-1.93	0.2521	128	0.1904	2748	X-RAY DIFFRACTION	100
1.93-1.95	0.2061	155	0.1887	2734	X-RAY DIFFRACTION	100
1.95-1.98	0.2063	142	0.1782	2728	X-RAY DIFFRACTION	100
1.98-2.01	0.2127	140	0.1734	2751	X-RAY DIFFRACTION	100
2.01-2.04	0.2003	148	0.1739	2736	X-RAY DIFFRACTION	100
2.04-2.08	0.2474	120	0.1733	2730	X-RAY DIFFRACTION	100
2.08-2.11	0.2216	142	0.1756	2776	X-RAY DIFFRACTION	100
2.11-2.15	0.2113	138	0.168	2725	X-RAY DIFFRACTION	100
2.15-2.19	0.2168	142	0.165	2784	X-RAY DIFFRACTION	100
2.19-2.24	0.1961	167	0.1631	2713	X-RAY DIFFRACTION	100
2.24-2.28	0.1966	166	0.1581	2709	X-RAY DIFFRACTION	100
2.28-2.34	0.1916	153	0.1547	2753	X-RAY DIFFRACTION	100
2.34-2.4	0.2252	144	0.1517	2755	X-RAY DIFFRACTION	100
2.4-2.46	0.1945	148	0.1487	2728	X-RAY DIFFRACTION	100
2.46-2.53	0.2079	119	0.1507	2787	X-RAY DIFFRACTION	100
2.53-2.61	0.1907	133	0.1479	2788	X-RAY DIFFRACTION	100
2.61-2.71	0.1891	151	0.1511	2750	X-RAY DIFFRACTION	100
2.71-2.82	0.1966	173	0.1505	2740	X-RAY DIFFRACTION	100
2.82-2.94	0.2092	140	0.1562	2798	X-RAY DIFFRACTION	100
2.94-3.1	0.186	126	0.1547	2789	X-RAY DIFFRACTION	100
3.1-3.29	0.225	165	0.1663	2778	X-RAY DIFFRACTION	100
3.29-3.55	0.2002	132	0.1583	2799	X-RAY DIFFRACTION	100
3.55-3.9	0.1969	138	0.1523	2814	X-RAY DIFFRACTION	100
3.91-4.47	0.1402	163	0.1313	2818	X-RAY DIFFRACTION	100
4.47-5.63	0.1791	151	0.146	2857	X-RAY DIFFRACTION	100
5.63-42.59	0.2113	162	0.2078	2966	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	0.8435	0.3534	0.0793	0.5174	0.1101	0.935	0.0626	-0.0559	-0.0361	0.1651	0.0449	-0.1528	-0.001	0.1857	0.0006	0.2048	0.0062	-0.056	0.2424	0.0008	0.2501	11.528	20.996	58.575
2	0.4099	0.2479	0.0773	0.7325	-0.0907	1.5391	-0.0087	0.0217	0.0177	0.0957	0.0427	-0.0651	-0.1254	0.0784	0	0.1931	0.0048	-0.0078	0.1993	-0.0046	0.2155	3.702	21.455	45.724
3	0.0886	0.0448	0.0464	-0.0782	0.0307	-0.0052	-0.0346	0.0193	0.1167	0.1815	0.0729	0.0633	0.2	0.1197	-0	0.3111	-0.0034	-0.0072	0.2064	0.0073	0.2573	-3.644	45.909	48.417
4	0.1272	-0.2362	0.0636	0.3276	-0.1045	0.2745	-0.0129	-0.0026	0.026	0.0906	0.0614	-0.0316	-0.0284	-0.0453	0	0.2414	-0.0001	-0.0057	0.2324	0.0039	0.2269	-8.507	26.442	51.812
5	1.1454	0.3157	0.1781	0.6924	-0.1772	0.7325	0.091	-0.2643	-0.1793	0.5165	0.0079	0.2292	0.1434	-0.2109	0.0472	0.4403	-0.0113	0.0759	0.3299	0.0053	0.1969	-3.909	64.253	61.476
6	0.579	0.1359	0.1012	0.5527	-0.2506	0.9376	-0.0311	-0.055	-0.0152	0.1824	0.0931	0.0939	0.0507	-0.0682	0	0.2432	0.0087	0.0255	0.219	0.0138	0.1978	-1.939	65.869	45.581
7	-0.091	0.1354	-0.1449	0.0004	-0.0711	-0.0549	0.0044	-0.0635	-0.0826	-0.0499	-0.0552	-0.1988	0.0398	-0.1059	-0	0.3325	-0.0434	0.0063	0.2402	0.0301	0.2713	6.58	46.246	49.933
8	0.2027	-0.1428	0.0451	0.3015	-0.0752	0.3359	-0.0441	-0.0995	-0.0561	0.2342	0.0786	-0.0886	0.0972	0.0275	0	0.3026	0.0125	-0.0202	0.2625	0.0083	0.2265	12.499	57.247	47.051
9	0.2447	-0.2208	-0.1061	0.2129	0.1073	0.0569	0.0312	-0.1578	-0.1244	0.4529	-0.0733	-0.1448	0.0727	0.0388	-0.0001	0.3434	0.0025	0.0676	0.2858	0.0135	0.2545	-23.913	20.533	66.595
10	0.2904	0.2272	0.066	0.3378	0.3083	0.4097	0.2616	-0.2056	-0.275	0.6342	0.0421	0.0365	0.3528	-0.0956	0.0397	0.3309	-0.0562	0.0882	0.251	0.0305	0.2849	-31.776	17.543	68.653
11	0.4106	0.0728	0.3607	2.3388	-1.6593	1.5438	-0.1194	-0.1585	-0.0075	0.8556	0.1736	0.7908	-0.6009	-0.6093	-0.061	0.2133	0.0909	0.1722	0.3802	0.0609	0.4505	-39.638	26.721	62.096
12	0.5868	0.0151	-0.2352	0.5663	-0.3605	0.2822	-0.1115	0.0583	0.1348	0.4803	0.0735	0.5875	0.2472	-0.066	0.0215	0.1373	-0.0354	0.0535	0.2526	0.0173	0.3028	-31.72	16.202	51.752
13	0.1815	-0.1382	-0.1968	0.0758	0.0344	0.419	0.0832	-0.0554	0.0101	0.1391	-0.1127	0.2384	-0.0573	-0.3335	0.0023	0.223	0.0319	0.0233	0.3032	0.0047	0.3107	-34.418	25.124	51.11
14	0.2595	-0.073	0.2752	0.0828	-0.1205	0.2495	-0.0095	0.0941	0.0102	-0.2223	0.1598	-0.0315	-0.1208	0.036	0	0.2223	-0.0081	0.0251	0.2467	0.0138	0.274	-23.056	17.357	48.165
15	0.0708	0.0564	-0.0705	0.0638	-0.1352	0.2242	-0.0116	-0.0681	0.0909	-0.1594	-0.0808	0.4553	-0.1423	-0.1913	-0	0.2045	0.0183	0.0093	0.2381	-0.0041	0.2527	-25.986	24.713	46.204
16	0.3544	0.0307	0.0573	0.0414	-0.0453	0.372	0.1763	-0.0953	-0.1671	0.4621	-0.25	0.515	0.2156	-0.183	0	0.2847	-0.0355	0.0314	0.2434	0.0116	0.2975	-21.157	15.859	54.416
17	0.0229	0.0129	-0.0043	0.0368	-0.0202	0.0087	0.0013	0.0889	-0.4744	0.2236	0.169	0.2281	0.4712	0.1514	0.0001	0.3783	-0.0301	0.0067	0.254	0.0071	0.3409	-18.1	-3.381	46.701
18	0.0907	-0.0845	-0.142	0.1712	-0.0379	0.3271	0.0153	-0.0278	-0.0475	0.1244	0.0399	0.0679	0.1176	-0.0459	-0	0.22	0.0089	0.0036	0.2319	0.0099	0.2265	-14.586	15.039	53.613
19	0.2188	-0.0805	0.0177	0.4192	0.2427	0.1573	-0.1299	-0.4059	0.2362	0.4709	0.0707	-0.1743	-0.0196	0.2346	-0.1099	0.4063	-0	-0.1993	0.368	-0.0335	0.3661	35.449	65.561	57.427
20	0.0602	-0.06	0.0937	0.2359	-0.054	0.4447	0.0267	0.2822	-0.2493	0.0802	0.1926	-0.6361	0.1285	0.9415	0.5856	0.2885	0.0898	-0.2417	0.5491	-0.0182	0.5868	46.052	58.583	48.285
21	0.3001	-0.0116	0.0919	0.3931	0.4461	0.5664	-0.0449	-0.0499	-0.0659	0.3947	-0.0417	-0.5247	-0.0984	0.325	0.0001	0.2069	-0.0069	-0.0828	0.3336	0.0083	0.3647	36.504	63.463	40.646
22	0.1178	-0.1365	-0.3058	0.1392	0.2951	0.5078	-0.0728	-0.0694	0.0466	0.1013	0.08	-0.1934	0.0077	-0.0427	0	0.2557	-0.0228	-0.049	0.2788	0.0014	0.299	25.773	67.99	40.695
23	0.2467	-0.0024	0.1309	0.1689	-0.3007	0.4288	0.0119	-0.0326	0.0033	0.205	0.0238	-0.1653	-0.0128	0.1571	0	0.2559	0.0049	-0.0485	0.2729	-0.0079	0.2858	26.823	63.9	41.715
24	0.0726	0.0745	0.0305	0.035	0.0209	0.0055	-0.1958	0.2385	0.2068	-0.0375	-0.0328	0.1837	-0.8903	-0.0343	0.0001	0.4744	-0.0732	-0.0013	0.28	0.0049	0.3567	20.49	88.817	40.58
25	0.262	-0.1626	0.0788	0.1586	0.0687	0.3295	-0.0117	-0.02	0.0307	0.2726	0.0597	0.0217	-0.113	0.0525	-0	0.3154	-0.0079	-0.0455	0.2668	-0.0183	0.2434	19.422	70.252	48.492

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 4:72 )	A	4 - 72
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 73:185 )	A	73 - 185
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 186:205 )	A	186 - 205
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 206:251 )	A	206 - 251
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 4:72 )	B	4 - 72
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 73:168 )	B	73 - 168
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 169:200 )	B	169 - 200
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 201:251 )	B	201 - 251
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 4:30 )	C	4 - 30
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 31:49 )	C	31 - 49
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 50:72 )	C	50 - 72
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 73:95 )	C	73 - 95
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 96:124 )	C	96 - 124
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 125:144 )	C	125 - 144
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 145:168 )	C	145 - 168
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 169:193 )	C	169 - 193
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 194:205 )	C	194 - 205
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 206:251 )	C	206 - 251
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 4:49 )	D	4 - 49
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 50:72 )	D	50 - 72
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 73:124 )	D	73 - 124
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 125:144 )	D	125 - 144
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 145:193 )	D	145 - 193
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 194:205 )	D	194 - 205
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 206:251 )	D	206 - 251

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