PDB-4d5u: Structure of OmpF in I2

ID or keywords:

Entry

Database: PDB / ID: 4d5u

Title

Structure of OmpF in I2

Components

OUTER MEMBRANE PROTEIN F

Keywords

STRUCTURAL PROTEIN /

PORIN

Function / homology

Function and homology information

colicin transmembrane transporter activity / monoatomic ion channel complex /

porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport /

lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity ...
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Chaptal, V. / Kilburg, A. / Flot, D. / Wiseman, B. / Aghajari, N. / Jault, J.M. / Falson, P.

Citation

Journal: Biochim.Biophys.Acta / Year: 2016
Title: Two Different Centered Monoclinic Crystals of the E. Coli Outer-Membrane Protein Ompf Originate from the Same Building Block.
Authors: Chaptal, V. / Kilburg, A. / Flot, D. / Wiseman, B. / Aghajari, N. / Jault, J. / Falson, P.

History

Deposition	Nov 7, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 20, 2016	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4d5u.cif.gz	791 KB	Display	PDBx/mmCIF format
PDB format	pdb4d5u.ent.gz	676.9 KB	Display	PDB format
PDBx/mmJSON format	4d5u.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/d5/4d5u ftp://data.pdbj.org/pub/pdb/validation_reports/d5/4d5u	HTTPS FTP

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Related structure data

Related structure data	2zfgS 4jfb S: Starting model for refinement
Similar structure data	4lse-d 1gfq-1 3pou-1 3k19-3 3k19-4 1opf-2 4lsf-1 3k19-2 6wtz-d 3k1b-1 3k1b-2 2omf-1 4gcp-2 6zhp-1 3hwb-1 4lsf-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

Related structure data

2zfgS

4jfb

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: OUTER MEMBRANE PROTEIN F

B: OUTER MEMBRANE PROTEIN F

C: OUTER MEMBRANE PROTEIN F

D: OUTER MEMBRANE PROTEIN F

E: OUTER MEMBRANE PROTEIN F

F: OUTER MEMBRANE PROTEIN F

223 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: OUTER MEMBRANE PROTEIN F

B: OUTER MEMBRANE PROTEIN F

C: OUTER MEMBRANE PROTEIN F

defined by author&software
111 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: OUTER MEMBRANE PROTEIN F

E: OUTER MEMBRANE PROTEIN F

F: OUTER MEMBRANE PROTEIN F

defined by author&software
111 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	159.730, 115.690, 222.854
Angle α, β, γ (deg.)	90.00, 104.95, 90.00
Int Tables number	5
Space group name H-M	I121

#1: Protein	OUTER MEMBRANE PROTEIN F / OUTER MEMBRANE PROTEIN 1A / OUTER MEMBRANE PROTEIN B / OUTER MEMBRANE PROTEIN IA / PORIN OMPF / OMPF Mass: 37114.250 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: THIS IS THE MATURE FORM OF WILD-TYPE OMPF EXTRACTED FROM E. COLI, WITHOUT MODIFICATIONS TO THE PROTEIN. AMINO-ACID ALA1 IS THE FIRST AMINO-ACID OF THE PROTEIN, THE FIRST 22 ARE OF A SIGNAL ...Details: THIS IS THE MATURE FORM OF WILD-TYPE OMPF EXTRACTED FROM E. COLI, WITHOUT MODIFICATIONS TO THE PROTEIN. AMINO-ACID ALA1 IS THE FIRST AMINO-ACID OF THE PROTEIN, THE FIRST 22 ARE OF A SIGNAL PEPTIDE BEING CLEAVED OFF. Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P02931
Sequence details	AMINO-ACID ALA1 IN THE COORDINATE FILE IS THE FIRST AMINO- ACID OF THE MATURE PROTEIN. THE 22 ...AMINO-ACID ALA1 IN THE COORDINATE FILE IS THE FIRST AMINO- ACID OF THE MATURE PROTEIN. THE 22 PREVIOUS AMINO-ACIDS CORRESPOND TO A SIGNAL PEPTIDE THAT IS CLEAVED OFF.

#1: Protein

OUTER MEMBRANE PROTEIN F / OUTER MEMBRANE PROTEIN 1A / OUTER MEMBRANE PROTEIN B / OUTER MEMBRANE PROTEIN IA / PORIN OMPF / OMPF

Mass: 37114.250 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: THIS IS THE MATURE FORM OF WILD-TYPE OMPF EXTRACTED FROM E. COLI, WITHOUT MODIFICATIONS TO THE PROTEIN. AMINO-ACID ALA1 IS THE FIRST AMINO-ACID OF THE PROTEIN, THE FIRST 22 ARE OF A SIGNAL ...
Source: (natural)

ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P02931

Sequence details

AMINO-ACID ALA1 IN THE COORDINATE FILE IS THE FIRST AMINO- ACID OF THE MATURE PROTEIN. THE 22 ...

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.3 Å³/Da / Density % sol: 71.3 % / Description: NONE
Crystal grow	pH: 8 Details: 16% PEG 4000, 0.4 M NACL AND 10 MM CDCL2 AS AN ADDITIVE, pH 8

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Data collection

Diffraction	Mean temperature: 140 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.5→25 Å / Num. obs: 48149 / % possible obs: 97.6 % / Observed criterion σ(I): 1.8 / Redundancy: 2.5 % / R_merge(I) obs: 0.17 / Net I/σ(I): 4.5
Reflection shell	Resolution: 3.5→3.61 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.2_1309)	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZFG

2zfg

Resolution: 3.5→24.834 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 32.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2827	2437	5.1 %
R_work	0.2293	-	-
obs	0.232	48149	97.2 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.5→24.834 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15762	0	0	0	15762

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	16101
X-RAY DIFFRACTION	f_angle_d	1.252	21785
X-RAY DIFFRACTION	f_dihedral_angle_d	12.925	5629
X-RAY DIFFRACTION	f_chiral_restr	0.056	2210
X-RAY DIFFRACTION	f_plane_restr	0.007	2940

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 (%)
3.5-3.5712	0.3528	131	0.2917	2670	X-RAY DIFFRACTION	97
3.5712-3.6487	0.3766	161	0.2935	2657	X-RAY DIFFRACTION	97
3.6487-3.7333	0.362	141	0.2904	2671	X-RAY DIFFRACTION	97
3.7333-3.8263	0.3215	158	0.2787	2633	X-RAY DIFFRACTION	97
3.8263-3.9294	0.3412	118	0.2708	2684	X-RAY DIFFRACTION	97
3.9294-4.0445	0.3204	139	0.2459	2691	X-RAY DIFFRACTION	98
4.0445-4.1745	0.2853	132	0.2338	2687	X-RAY DIFFRACTION	97
4.1745-4.3229	0.2847	139	0.2074	2711	X-RAY DIFFRACTION	98
4.3229-4.495	0.221	143	0.183	2682	X-RAY DIFFRACTION	98
4.495-4.6983	0.2572	173	0.1822	2696	X-RAY DIFFRACTION	98
4.6983-4.9442	0.2245	143	0.1781	2693	X-RAY DIFFRACTION	98
4.9442-5.2512	0.238	139	0.1701	2725	X-RAY DIFFRACTION	98
5.2512-5.6522	0.2312	152	0.1803	2693	X-RAY DIFFRACTION	98
5.6522-6.2129	0.2808	156	0.2063	2670	X-RAY DIFFRACTION	97
6.2129-7.0936	0.2705	148	0.208	2710	X-RAY DIFFRACTION	97
7.0936-8.869	0.2656	126	0.23	2750	X-RAY DIFFRACTION	97
8.869-24.8344	0.3175	138	0.3	2689	X-RAY DIFFRACTION	94

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	3.2518	-0.3115	0.083	1.753	1.2233	1.6551	-0.3916	-0.0042	-0.2259	0.4644	-0.0346	-0.6437	-0.5199	1.0221	-0.2295	0.4162	-0.045	0.025	0.4847	-0.1375	0.4414	70.2305	-27.2827	32.3875
2	2.247	-0.3607	-1.5281	1.4038	0.2696	3.5245	-0.0424	0.4111	0.2886	0.1918	-0.6238	-0.4324	-0.421	1.3366	-0.0654	0.3187	0.0711	-0.0509	0.5512	-0.0104	0.4155	74.8949	-37.8279	36.1678
3	1.7084	-0.1876	-0.8719	2.5759	-0.7911	3.5079	0.0754	-0.3755	0.0352	-0.3032	0.0175	-0.3898	-0.1699	1.0196	-0.3027	0.3954	-0.0953	0.0214	1.1073	0.0467	0.474	90.8064	-32.781	36.2346
4	0.9799	-0.3874	-1.3933	1.6097	0.5591	4.6009	0.0603	-0.3342	0.0862	0.0316	-0.2448	-0.2376	-0.2447	1.2129	-0.4695	0.641	-0.3468	0.0984	1.4682	-0.0357	0.309	93.1856	-22.8032	31.6031
5	2.8023	-0.3566	-1.1635	1.6473	-0.0336	2.2675	0.6006	-1.1413	0.9698	-0.317	-0.1826	-0.0775	-0.9073	1.7473	-0.4548	0.7981	-0.3699	-0.0273	0.9776	-0.0706	0.4868	80.8281	-14.7797	30.5454
6	2.5001	0.8485	-0.0462	1.2651	0.5274	4.2337	0.2206	0.8119	-0.2585	-0.2977	0.3734	-0.0726	0.1427	-1.0675	1.1114	0.5174	-0.6178	0.3536	1.2645	-0.0606	0.5676	52.7898	-41.3461	23.9811
7	2.0433	0.2786	-0.2323	1.3433	-0.7822	3.6888	-0.2697	0.5009	-0.4721	0.1259	0.1046	0.4568	-0.148	-1.1183	-0.2861	0.1819	-0.1698	-0.0656	0.6194	-0.0577	0.3286	57.9943	-30.9617	27.498
8	1.4081	-0.1643	0.5291	1.8799	0.2197	3.133	-0.1263	0.9207	-0.1817	-0.0848	0.2294	0.0617	-0.5589	-0.7978	-0.4261	0.8746	0.1428	0.021	1.5654	0.1426	0.3263	50.785	-21.4871	15.9034
9	0.2322	0.05	-0.3977	0.0248	-0.2522	1.7437	-0.0314	0.9777	-0.0512	-0.2953	0.1149	0.0528	-0.4751	-0.6944	0.5683	0.2466	0.1112	-0.3614	2.4147	0.1451	0.2287	45.0522	-26.4758	7.4846
10	0.7113	-0.3425	-0.8959	0.9209	0.1827	1.2132	0.2386	0.5988	-0.1888	-0.4529	0.2681	0.454	0.2688	-1.5465	-0.0456	0.5285	-0.4409	0.0493	2.236	-0.2776	0.6176	41.7561	-40.3042	11.7213
11	0.4533	0.4658	1.1961	2.5652	0.6181	3.8008	0.3125	0.3635	-0.0492	-0.4265	0.1768	-0.4212	0.9352	0.0385	2.39	0.8253	-0.0546	0.1311	0.8466	0.0844	0.5596	72.1026	-50.8729	34.074
12	0.8325	0.157	-0.0603	1.0715	0.2887	2.9903	-0.4191	0.9577	-1.0658	0.0904	0.0135	0.0044	0.9164	-0.3484	-0.0558	0.5736	-0.3824	0.1103	0.5592	-0.3254	0.642	60.8804	-50.6518	29.4815
13	2.2093	-0.6081	-0.8106	1.8748	-0.3853	2.8925	-0.4309	0.471	-0.5191	-0.2264	0.2203	-0.1743	1.2781	-0.4763	0.2994	1.1772	-0.1954	0.3261	0.8786	-0.429	1.1098	61.4813	-65.7648	22.6126
14	0.103	0.1635	-0.134	0.1874	-0.011	1.2057	-0.1429	0.5356	-0.6026	-0.2849	-0.1124	0.1056	1.0159	0.023	-1.2125	1.8588	0.1323	0.541	0.2045	-0.6362	1.2206	71.4289	-71.0164	22.0489
15	1.4156	-0.3168	-0.5853	1.0736	0.0201	2.4717	-0.5451	0.8659	-0.9516	0.5775	-0.0765	-0.0103	2.3547	-0.2283	-0.073	1.3458	0.3668	0.4659	0.9734	-0.1317	1.1433	80.5908	-64.8841	31.9491
16	4.596	0.6573	-0.4724	1.1284	-0.2724	3.1115	-0.1029	0.3762	-0.1433	0.0446	-0.238	0.0802	0.1444	-0.5388	-0.0902	0.7593	-0.055	0.0078	0.3658	0.0849	0.5166	53.1387	-26.0443	71.752
17	2.1427	0.458	-0.4251	0.521	-0.9572	1.7005	-0.1212	0.5597	-0.3955	0.4494	-0.1481	0.4133	0.0202	0.3997	0.2204	0.7227	-0.2338	0.0768	0.2627	-0.1515	0.5352	59.2677	-36.2399	73.4708
18	2.5337	-0.5688	0.5621	3.0138	1.1711	3.2186	-0.1545	0.2211	-0.4804	0.041	0.1667	0.1659	0.707	-1.4671	-0.1548	0.837	-0.3029	0.1781	0.7765	-0.1976	0.7737	45.8129	-45.9908	74.6313
19	1.6524	-1.6532	1.3311	1.802	-1.0326	2.5621	-0.3599	-0.0406	-0.5703	0.0891	0.5708	0.4036	0.1991	-0.197	0.1176	0.4686	-0.6123	0.0523	1.2929	-0.1924	0.6705	35.6334	-41.1364	75.4021
20	3.0678	1.1066	-0.7817	2.2528	-1.5764	2.4911	-0.2594	0.8451	-0.064	0.0108	0.3044	0.2547	0.2535	-1.9463	-0.0226	0.8062	-0.0409	0.0513	1.2138	-0.0802	0.5615	36.6225	-27.2062	70.5695
21	1.6636	-0.0284	0.1689	2.4537	1.0704	2.7846	0.4756	-0.5991	0.2418	-0.0428	0.2073	-0.2494	-0.9249	0.4103	0.4326	0.6197	-0.2662	0.163	1.0158	-0.195	0.6327	72.6142	-16.0088	81.1392
22	1.4989	-0.2193	-0.9321	0.5943	0.8503	2.0659	0.2909	0.2123	0.5378	-0.1577	-0.3043	-0.4778	-1.0634	0.0628	-0.3553	0.8594	-0.081	0.0975	0.6104	-0.0995	0.5907	62.2418	-16.3641	74.8229
23	2.085	-1.1387	1.2507	2.4431	-0.5814	1.745	0.4757	-0.1526	0.4633	-0.0695	-0.1428	0.165	-1.3105	0.1416	-0.5198	1.501	-0.066	0.1513	0.7445	-0.0538	0.63	56.7331	-1.4834	80.0531
24	2.7643	0.0829	1.0176	0.6766	-0.9235	1.7285	0.0061	-0.7098	0.8158	-0.1674	0.3132	0.2377	-1.2149	-0.4166	-0.8412	1.9185	-0.2441	0.499	0.4144	-0.1999	0.7796	62.2777	3.7333	88.4238
25	1.6222	0.3609	0.2145	1.5023	-0.9869	2.9282	0.6758	-0.0813	0.5441	-0.2699	0.3783	-0.2709	-2.1757	-0.0778	-0.4282	1.3959	-0.6859	0.2003	1.133	-0.1977	0.5688	75.9457	-2.086	89.4867
26	2.1934	-0.9134	1.2132	2.1279	0.7405	1.5614	-0.0123	0.0595	-0.3081	-0.1855	-0.292	-0.1018	0.6681	0.7616	-0.3054	0.9079	-0.1031	0.1656	0.6849	-0.2775	0.4459	70.5861	-39.7088	80.1392
27	1.3601	-0.7506	0.5069	2.0984	-0.3314	1.8845	-0.1606	-0.3625	-0.9685	-0.1418	-0.2865	-0.6562	-0.0226	0.9686	-0.2966	0.5538	-0.2176	0.0259	0.9487	-0.1006	0.4305	76.262	-29.1116	81.5956
28	0.8111	0.259	0.3984	4.2921	-0.2844	0.2756	-0.0294	-0.5492	-0.0419	0.6343	0.1399	0.1253	0.0937	1.3115	0.0998	0.5749	-0.0468	0.0168	1.5627	-0.0332	0.5209	86.2195	-34.2238	94.0044
29	1.7308	0.2169	-0.2416	1.1309	0.1595	2.4672	-0.1718	0.1288	-0.4597	0.1169	-0.511	-0.4439	0.7877	0.8832	0.0447	0.7728	0.5337	0.0249	1.5671	0.1803	0.5855	84.1325	-44.3267	98.6557
30	0.9104	0.6183	0.4983	2.1962	-0.4518	0.611	0.2624	-0.1814	-0.2406	0.0385	0.0775	-0.0341	1.2247	1.7057	0.1322	1.0048	0.4315	0.2444	1.0021	0.0157	0.7646	75.8619	-52.3498	89.2938

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:35)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 36:101)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 102:208)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 209:261)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 262:340)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 1:35)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 36:101)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 102:208)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 209:261)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 262:340)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 1:35)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 36:101)
13	X-RAY DIFFRACTION	13	(CHAIN C AND RESID 102:208)
14	X-RAY DIFFRACTION	14	(CHAIN C AND RESID 209:261)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 262:340)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 1:35)
17	X-RAY DIFFRACTION	17	(CHAIN D AND RESID 36:101)
18	X-RAY DIFFRACTION	18	(CHAIN D AND RESID 102:208)
19	X-RAY DIFFRACTION	19	(CHAIN D AND RESID 209:261)
20	X-RAY DIFFRACTION	20	(CHAIN D AND RESID 262:340)
21	X-RAY DIFFRACTION	21	(CHAIN E AND RESID 1:35)
22	X-RAY DIFFRACTION	22	(CHAIN E AND RESID 36:101)
23	X-RAY DIFFRACTION	23	(CHAIN E AND RESID 102:208)
24	X-RAY DIFFRACTION	24	(CHAIN E AND RESID 209:261)
25	X-RAY DIFFRACTION	25	(CHAIN E AND RESID 262:340)
26	X-RAY DIFFRACTION	26	(CHAIN F AND RESID 1:35)
27	X-RAY DIFFRACTION	27	(CHAIN F AND RESID 36:101)
28	X-RAY DIFFRACTION	28	(CHAIN F AND RESID 102:208)
29	X-RAY DIFFRACTION	29	(CHAIN F AND RESID 209:261)
30	X-RAY DIFFRACTION	30	(CHAIN F AND RESID 262:340)

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