PDB-9nt4: Crystal structure of ecLacI transcription factor ancestor 1 bound...

ID or keywords:

Entry

Database: PDB / ID: 9nt4

Title

Crystal structure of ecLacI transcription factor ancestor 1 bound to d-fucose

Components

LacI Transcription Factor

Keywords

TRANSCRIPTION / Ancestral sequence reconstruction / transcription factor / LacI / d-fucose

Function / homology

beta-D-fucopyranose

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Georgelin, R.L. / Frkic, R.L. / Jackson, C.J.

Funding support

Australia, 2items

Citation

Journal: To Be Published
Title: Crystal structure of ecLacI transcription factor ancestor 1 bound to d-fucose
Authors: Georgelin, R. / Frkic, R.L. / Jackson, C.J.

History

Deposition	Mar 18, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 18, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9nt4.cif.gz	799.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9nt4.ent.gz	670.1 KB	Display	PDB format
PDBx/mmJSON format	9nt4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nt/9nt4 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/9nt4	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LacI Transcription Factor

B: LacI Transcription Factor

C: LacI Transcription Factor

D: LacI Transcription Factor

E: LacI Transcription Factor

F: LacI Transcription Factor

G: LacI Transcription Factor

H: LacI Transcription Factor

hetero molecules

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

1

A: LacI Transcription Factor

H: LacI Transcription Factor

hetero molecules

defined by author&software
Evidence: gel filtration
61.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: LacI Transcription Factor

F: LacI Transcription Factor

hetero molecules

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

3

C: LacI Transcription Factor

E: LacI Transcription Factor

hetero molecules

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

4

D: LacI Transcription Factor

G: LacI Transcription Factor

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.446, 210.997, 87.315
Angle α, β, γ (deg.)	90.00, 90.51, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

LacI Transcription Factor

Mass: 30698.393 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Production host:

Escherichia coli (E. coli)

#2: Sugar

ChemComp-FCB / beta-D-fucopyranose / beta-D-fucose / 6-deoxy-beta-D-galactopyranose / D-fucose / fucose

Type: D-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₂O₅ / Feature type: SUBJECT OF INVESTIGATION

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.31 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 15%w/v PEG 4000, 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.4→43.66 Å / Num. obs: 88505 / % possible obs: 99.1 % / Redundancy: 7.1 % / CC_1/2: 0.994 / R_merge(I) obs: 0.199 / R_pim(I) all: 0.08 / R_rim(I) all: 0.215 / Χ²: 1 / Net I/σ(I): 8.4 / Num. measured all: 629149
Reflection shell	Resolution: 2.4→2.44 Å / % possible obs: 98.6 % / Redundancy: 7.3 % / R_merge(I) obs: 1.285 / Num. measured all: 33242 / Num. unique obs: 4558 / CC_1/2: 0.395 / R_pim(I) all: 0.509 / R_rim(I) all: 1.383 / Χ²: 0.91 / Net I/σ(I) obs: 1.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→43.66 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2701	4413	4.99 %
R_work	0.2187	-	-
obs	0.2212	88448	99.05 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→43.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15998	0	88	67	16153

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005
X-RAY DIFFRACTION	f_angle_d	0.688
X-RAY DIFFRACTION	f_dihedral_angle_d	5.132	2240
X-RAY DIFFRACTION	f_chiral_restr	0.046	2571
X-RAY DIFFRACTION	f_plane_restr	0.007	3024

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 (%)
2.4-2.43	0.3247	151	0.2933	2811	X-RAY DIFFRACTION	99
2.43-2.46	0.3419	140	0.2943	2755	X-RAY DIFFRACTION	98
2.46-2.49	0.3465	159	0.3141	2757	X-RAY DIFFRACTION	99
2.49-2.52	0.3697	166	0.2974	2780	X-RAY DIFFRACTION	98
2.52-2.55	0.3764	171	0.2993	2756	X-RAY DIFFRACTION	99
2.55-2.59	0.3657	164	0.2886	2726	X-RAY DIFFRACTION	99
2.59-2.62	0.3251	166	0.2833	2795	X-RAY DIFFRACTION	99
2.62-2.66	0.348	127	0.2827	2808	X-RAY DIFFRACTION	99
2.66-2.7	0.334	125	0.2729	2780	X-RAY DIFFRACTION	99
2.7-2.75	0.3138	151	0.2889	2816	X-RAY DIFFRACTION	99
2.75-2.79	0.3418	173	0.2698	2746	X-RAY DIFFRACTION	99
2.79-2.85	0.3321	147	0.26	2793	X-RAY DIFFRACTION	99
2.85-2.9	0.2908	150	0.2562	2823	X-RAY DIFFRACTION	99
2.9-2.96	0.321	165	0.2508	2730	X-RAY DIFFRACTION	99
2.96-3.02	0.3264	175	0.2432	2810	X-RAY DIFFRACTION	99
3.02-3.09	0.2944	134	0.2529	2775	X-RAY DIFFRACTION	99
3.09-3.17	0.3024	145	0.2614	2823	X-RAY DIFFRACTION	99
3.17-3.26	0.3236	132	0.2466	2795	X-RAY DIFFRACTION	99
3.26-3.35	0.2995	169	0.2359	2809	X-RAY DIFFRACTION	99
3.35-3.46	0.2752	116	0.2064	2796	X-RAY DIFFRACTION	99
3.46-3.58	0.2564	150	0.2037	2810	X-RAY DIFFRACTION	99
3.58-3.73	0.2526	153	0.2015	2827	X-RAY DIFFRACTION	99
3.73-3.9	0.2466	141	0.1937	2794	X-RAY DIFFRACTION	99
3.9-4.1	0.2317	154	0.1794	2801	X-RAY DIFFRACTION	99
4.1-4.36	0.2017	123	0.1672	2853	X-RAY DIFFRACTION	99
4.36-4.7	0.1951	151	0.1679	2820	X-RAY DIFFRACTION	100
4.7-5.17	0.2224	108	0.1699	2879	X-RAY DIFFRACTION	100
5.17-5.91	0.2394	143	0.1918	2832	X-RAY DIFFRACTION	100
5.91-7.45	0.2504	124	0.2081	2858	X-RAY DIFFRACTION	100
7.45-43.66	0.217	140	0.1933	2877	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	3.4457	-0.6754	-0.0623	4.9889	-2.2015	2.4533	0.2691	-0.4797	0.2103	0.8967	-0.1481	-0.2473	-0.1829	0.1218	-0.1384	0.5292	-0.0308	-0.0679	0.3017	-0.0305	0.4434	36.5056	26.1688	77.1449
2	2.7785	0.0708	-0.3384	3.0313	-0.9016	2.7246	0.0482	-0.0614	-0.2984	0.0398	-0.0269	-0.1159	-0.0079	0.1432	-0.0555	0.2256	0.0037	-0.023	0.216	0.0403	0.3054	36.1164	49.5648	59.8133
3	0.2292	0.5014	-0.0944	5.4022	-4.6079	4.0192	-0.1366	-0.0291	-0.1089	-0.7082	-0.2161	-1.0053	0.6091	0.1536	0.3359	0.3589	0.0521	0.0217	0.3252	-0.0188	0.4314	39.1721	34.2114	58.1089
4	2.5101	-0.7478	-0.4183	7.0331	2.4959	1.7457	-0.2047	-0.3929	0.0406	-0.309	0.4105	-0.1331	-0.187	0.4041	-0.2892	0.3107	0.0226	0.0221	0.318	0.0629	0.5902	0.4399	12.6076	31.2532
5	4.2862	-0.8546	-0.3637	5.1802	0.0448	2.7746	-0.369	-0.8071	-0.2395	1.2092	0.2384	0.3651	0.2818	-0.292	0.169	0.6225	0.0375	0.2204	0.455	0.0057	0.5715	-7.518	11.6005	41.5195
6	2.4031	-0.7449	0.8703	3.9077	-1.6196	1.2439	-0.2136	-0.4225	0.5036	-0.16	0.1562	0.9823	-0.751	-0.1535	-0.0651	0.1857	0.0176	0.0374	0.3061	-0.0339	0.5839	-12.6733	-0.5945	20.0005
7	4.0525	-0.9868	1.1947	3.3934	0.0306	3.5902	-0.1195	-0.6973	0.2635	0.3335	-0.066	0.3691	-0.0481	-0.6472	0.2316	0.2158	-0.0007	0.0401	0.2749	-0.07	0.3459	-11.9051	-10.4508	22.2817
8	1.9934	0.4628	0.9089	2.3127	0.7852	2.4434	0.0882	-0.0935	-0.011	0.0776	0.0119	-0.193	0.2057	0.0042	-0.0773	0.2452	-0.0079	0.0242	0.2087	-0.0572	0.2612	0.8641	-13.084	20.9406
9	0.1908	-0.9117	-0.5097	4.505	2.3637	3.2436	-0.108	-0.1957	0.1698	-0.42	-0.3753	0.8919	-0.4857	-0.729	0.5193	0.3905	0.0945	0.0411	0.477	-0.1111	0.7357	-10.269	15.3267	24.5535
10	3.5506	3.3672	2.1909	3.8719	3.0422	3.0562	0.2242	-0.4569	-0.2752	-0.057	-0.6935	0.2997	-0.0304	-0.3764	0.3826	0.2779	0.005	0.0336	0.2056	-0.0809	0.3131	-2.3949	-17.4537	6.6946
11	6.2024	1.4397	-0.342	2.9781	0.7783	2.1643	-0.1245	-0.1319	-0.7623	0.2017	-0.0587	0.4319	0.1381	-0.8083	0.1385	0.3829	-0.102	0.096	0.8582	-0.1373	0.4977	2.2934	-26.2891	56.4085
12	0.8971	-0.2338	-0.4988	1.8581	0.7044	3.8951	-0.0603	-0.0443	-0.0111	0.001	-0.0155	0.0078	0.2239	-0.1129	0.0235	0.1683	0.0138	-0.0112	0.2618	-0.051	0.3296	27.1367	-25.848	44.0146
13	8.1015	0.1727	-1.5048	2.0517	0.0342	2.2644	-0.4072	0.6608	0.2156	0.0292	0.25	0.2705	0.0225	-0.7293	0.1743	0.3598	0.0627	-0.0578	0.5556	-0.0282	0.3046	13.5614	-19.2785	40.2123
14	6.9029	1.2709	2.0678	2.0379	0.3661	4.1635	0.3015	0.1981	-0.4897	0.0646	-0.154	-0.4927	0.5349	0.6675	-0.086	0.4696	-0.0099	-0.0703	0.4723	0.0876	0.3733	27.4177	54.6245	17.4423
15	4.6433	1.6919	-2.3218	4.9134	-2.4579	3.854	0.2469	0.7303	-1.0209	0.7139	-0.4231	-1.3183	0.2828	0.7194	0.0763	0.6299	-0.0375	-0.1313	0.6004	0.0703	0.5252	32.7003	50.5824	23.0652
16	2.5425	-1.7612	-1.3437	1.2077	0.932	0.7879	-0.1339	-0.9912	-1.9423	1.151	-0.0564	-0.5254	-0.1241	0.3481	0.0484	0.5192	-0.0445	-0.1017	0.5584	0.2425	0.6534	22.6024	47.5312	29.117
17	2.6633	0.5413	-1.8322	2.6094	-1.6951	3.6792	-0.2453	0.102	-0.2474	-0.166	0.1822	0.2033	0.518	-0.0882	0.0457	0.3371	-0.051	-0.0267	0.3117	0.0823	0.3838	1.3447	41.7566	16.1366
18	8.9335	1.5009	2.1525	1.4464	0.307	1.5474	-0.3286	-0.9054	-0.2134	0.1268	0.1082	-0.0717	-0.3271	-0.3323	0.1179	0.3293	-0.0104	0.0039	0.3965	0.0564	0.2815	13.852	54.5085	27.9386
19	3.2606	-0.1168	0.1131	1.6688	-0.17	3.4338	0.2777	0.0939	0.4347	0.5006	-0.1412	0.5254	-0.4368	-0.9651	-0.0884	0.5585	-0.0313	0.1971	0.7219	-0.1853	0.5894	3.4127	-12.8629	69.4913
20	3.2428	1.2336	2.0259	5.6507	1.5863	3.3173	-0.1828	0.1762	0.1408	0.0512	0.1643	-0.2117	-0.3475	0.1963	0.0162	0.3164	-0.0169	0.0057	0.2816	-0.0288	0.2506	31.6105	-4.1688	65.9778
21	5.4724	0.3564	-1.7361	1.5881	-0.6293	1.2795	-0.0957	-0.7371	-0.3631	0.3527	0.0229	0.0552	0.1793	0.2406	-0.0251	0.5151	-0.1005	0.0167	0.6222	-0.1652	0.3141	17.5038	-16.2543	76.853
22	5.6615	-1.7267	-2.2617	4.8438	2.1969	7.7654	-0.2051	0.4183	0.5768	0.4312	0.3197	-0.3568	-0.2619	-0.6748	-0.0944	0.3638	0.0841	-0.034	0.3818	-0.0653	0.4157	8.5451	12.7337	39.2827
23	1.3324	-1.1731	-1.1981	1.5993	1.378	1.358	-0.207	-0.4306	1.2795	0.2957	0.3104	-1.0463	-0.9128	0.0539	-0.1689	0.7508	0.0806	0.0318	0.4271	-0.2409	0.7861	14.3669	20.42	41.0863
24	3.5929	-1.0907	-0.5079	1.5019	0.636	1.6023	-0.024	0.1457	0.272	-0.0151	-0.0107	-0.1636	-0.163	0.0642	0.0292	0.1928	-0.0325	0.0194	0.2378	-0.0388	0.3326	26.4962	-2.7423	23.1535
25	2.3986	-1.3255	-0.4572	2.8596	0.8701	3.7318	-0.2508	-0.5002	0.3346	0.6573	0.2293	-0.1121	0.0459	0.1876	-0.0047	0.3166	0.016	-0.0212	0.3881	-0.1281	0.4118	19.5068	0.4892	40.5384
26	5.8557	1.0457	0.9104	2.6965	0.5881	2.4682	-0.1212	-0.3038	0.501	0.0475	0.1491	-0.2026	-0.1554	0.3234	-0.0199	0.3142	-0.0196	-0.0026	0.4504	0.0692	0.3066	29.7169	64.7364	9.0864
27	6.3672	2.9529	1.1416	4.5463	-2.8896	4.2663	0.3098	0.3785	0.9722	1.0598	0.5634	0.4163	-1.5255	0.2314	-0.2846	-0.002	-0.1041	0.0474	0.8431	0.2277	0.7993	27.2622	72.2349	-1.8397
28	2.2467	0.3323	0.3775	2.1352	-0.102	3.3466	0.0239	-0.0612	0.072	0.1588	0.0006	0.2062	-0.1561	-0.1489	-0.018	0.1882	0.0468	0.0113	0.1968	0.0419	0.2704	2.2229	64.3196	-4.5034
29	5.8269	1.1275	2.2059	2.6795	-0.0081	3.2755	0.1506	0.5683	-0.2418	0.1536	-0.0741	-0.1523	0.0799	0.5615	-0.0303	0.3212	0.0701	0.0773	0.4029	0.0281	0.2301	20.3099	59.8513	-7.5894
30	2.4195	-0.5822	0.264	3.6114	-1.966	3.3498	-0.0604	-0.1901	-0.9815	0.2363	0.5891	0.5836	0.703	0.6144	-0.4949	0.5234	0.1841	-0.0342	0.4232	0.0226	0.6314	22.313	23.2943	78.9166
31	0.2197	-0.2046	0.3913	1.6206	0.0772	0.8797	-0.698	-1.0931	-1.4609	0.2452	-0.1544	0.5582	0.3637	0.1553	-0.3483	0.4931	0.1218	0.2352	0.7008	0.5118	0.9867	10.9633	25.5408	80.8442
32	3.5367	-0.2279	-0.2491	1.4554	0.4067	1.9143	-0.1082	0.2839	-0.2448	-0.0159	0.0321	0.0673	0.0731	0.026	0.0847	0.2	-0.032	-0.0403	0.239	0.0229	0.3572	5.9885	42.3235	62.591
33	2.8403	-1.3861	-0.0922	2.7225	-1.0461	2.6873	-0.5198	-0.9305	-0.4719	0.7005	0.6585	0.4985	0.2003	-0.1824	-0.3215	0.4529	0.1096	0.09	0.5292	0.1481	0.4221	11.6352	37.2743	81.8279

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 59 through 146 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 147 through 289 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 290 through 335 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 63 through 90 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 91 through 146 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 147 through 175 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 176 through 205 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 206 through 289 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 290 through 321 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 322 through 336 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 62 through 146 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 147 through 289 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 290 through 335 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 62 through 115 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 116 through 142 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 143 through 160 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 161 through 289 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 290 through 330 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 61 through 160 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 161 through 289 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 290 through 330 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 61 through 104 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 105 through 160 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 161 through 278 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 279 through 330 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 59 through 124 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 125 through 160 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 161 through 289 )
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 290 through 333 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 62 through 124 )
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 125 through 160 )
32	X-RAY DIFFRACTION	32	chain 'H' and (resid 161 through 289 )
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 290 through 331 )

-
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