PDB-7pvh: Crystal structure of the folded domain of PorN

ID or keywords:

Entry

Database: PDB / ID: 7pvh

Title

Crystal structure of the folded domain of PorN

Components

Por secretion system protein porN/gldN

Keywords

PROTEIN TRANSPORT / secretion system / Porphyromonas gingivalis

Function / homology

Gliding motility associated protein GldN / Gliding motility associated protein GldN / Por secretion system protein porN/gldN

Function and homology information

Biological species

Porphyromonas gingivalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Fuchsbauer, O. / Roussel, A. / Leone, P.

Funding support

France, 1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: Structural and functional analyses of the Porphyromonas gingivalis type IX secretion system PorN protein.
Authors: Fuchsbauer, O. / Lunar Silva, I. / Cascales, E. / Roussel, A. / Leone, P.

History

Deposition	Oct 4, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 18, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 31, 2023	Group: Database references / Refinement description Category: citation / citation_author / pdbx_refine_tls_group Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_refine_tls_group.selection_details
Revision 1.2	Oct 16, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7pvh.cif.gz	187.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7pvh.ent.gz	149.4 KB	Display	PDB format
PDBx/mmJSON format	7pvh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7pvh_validation.pdf.gz	439.8 KB	Display	wwPDB validaton report
Full document	7pvh_full_validation.pdf.gz	444 KB	Display
Data in XML	7pvh_validation.xml.gz	17.8 KB	Display
Data in CIF	7pvh_validation.cif.gz	25.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pv/7pvh ftp://data.pdbj.org/pub/pdb/validation_reports/pv/7pvh	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: Por secretion system protein porN/gldN

B: Por secretion system protein porN/gldN

57.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	47.731, 132.538, 133.739
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Por secretion system protein porN/gldN Mass: 28926.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria) Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561 Gene: porN, PGN_1673 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RLE7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 33 mM Tris pH 8.5, 6.66% PEG 1000, 15.27% PEG 6000, 0.66 M citric acid pH 4.14

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 2→47 Å / Num. obs: 29165 / % possible obs: 98.3 % / Redundancy: 4 % / CC_1/2: 0.998 / Net I/σ(I): 1.5
Reflection shell	Resolution: 2→2.11 Å / Num. unique obs: 16566 / CC_1/2: 0.61

-
Processing

Software

Name	Version	Classification
BUSTER	2.10.3	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
SCALA		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→42.57 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.937 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU R_free Blow DPI: 0.16 / SU R_free Cruickshank DPI: 0.159

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.228	1466	5.13 %	RANDOM
R_work	0.196	-	-	-
obs	0.198	28568	98 %	-

Displacement parameters

B_iso max: 159.61 Å² / B_iso mean: 57.65 Å² / B_iso min: 24.39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.757 Å²	0 Å²	0 Å²
2-	-	7.6965 Å²	0 Å²
3-	-	-	-3.9395 Å²

Refine analyze

Luzzati coordinate error obs: 0.26 Å

Refinement step

Cycle: final / Resolution: 2→42.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3220	0	0	216	3436
B_iso mean	-	-	-	56.07	-
Num. residues	-	-	-	-	384

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	1144	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	96	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	469	HARMONIC	5
X-RAY DIFFRACTION	t_it	3306	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	418	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	3792	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	3306	HARMONIC	2	0.009
X-RAY DIFFRACTION	t_angle_deg	4487	HARMONIC	2	0.94
X-RAY DIFFRACTION	t_omega_torsion				2.96
X-RAY DIFFRACTION	t_other_torsion				16.81

LS refinement shell

Resolution: 2→2.08 Å / R_factor R_free error: 0 / Total num. of bins used: 14

	R_factor	Num. reflection	% reflection
R_free	0.2429	144	4.75 %
R_work	0.2281	2889	-
all	0.2288	3033	-
obs	-	-	99.8 %

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	0.1904	0.7348	3.6703	0.4318	6.524	-0.2546	-0.275	0.0986	0.3605	0.2923	-0.4822	0.0339	0.785	-0.0376	-0.0447	-0.0944	-0.0668	0.0465	0.0184	-0.1787	17.9213	30.5616	27.3936
2	13.6851	-8.1052	-7.0272	15.7888	-1.3587	11.1201	0.1387	-0.9001	0.3566	0.2059	0.182	0.7154	-0.8478	-0.7718	-0.3207	-0.017	0.0085	0.0733	0.0365	-0.0816	-0.1165	-1.5885	38.0372	23.0031
3	1.1002	-0.9091	0.9016	0.7947	-2.2679	12.1665	-0.066	-0.2353	0.2887	0.1291	0.0147	0.4254	-0.4811	-0.5903	0.0513	-0.102	0.0244	-0.0202	-0.1121	-0.0048	-0.0702	-3.3091	38.6591	12.7739
4	7.2041	0.5417	5.2995	8.8767	4.0768	0.7028	-0.0533	0.6909	0.6542	-0.2123	-0.0077	0.463	-0.5878	0.2647	0.061	0.2547	0.024	-0.0936	0.0466	0.0675	0.103	-2.9413	42.3499	4.2412
5	6.165	-1.7468	-2.42	3.3222	4.8607	6.1164	-0.0203	0.1418	0.0887	-0.2105	0.0454	0.1677	-0.2112	-0.1059	-0.0251	-0.0883	-0.0447	-0.0412	-0.0705	0.0188	-0.1689	4.2203	32.1713	5.0476
6	1.7149	0.1298	-0.0237	4.4808	-1.0816	4.2393	0.0617	0.081	-0.4738	-0.0716	-0.11	-0.0578	0.5889	0.2382	0.0483	-0.1145	0.0021	-0.0311	-0.0874	0.016	-0.0827	13.6188	22.6937	11.9848
7	9.2961	-6.671	5.0315	4.7723	-2.5193	1.0932	-0.0349	0.4856	-0.069	-0.1186	-0.0636	0.061	0.5963	0.5315	0.0985	0.0087	0.085	-0.0649	-0.0125	-0.0272	-0.042	14.0183	19.1526	6.0144
8	0.1583	5.2414	-9.1509	6.5712	-10.8393	10.5383	0.1839	-0.0462	-1.0064	0.6328	0.0358	-0.3631	0.7633	0.5244	-0.2197	0.0931	0.0013	-0.1319	-0.0567	-0.0385	0.0353	2.8138	17.919	4.1396
9	5.9908	-0.5509	4.4199	6.0905	4.3256	0	0.1924	0.2697	-0.4986	0.3153	0.0287	0.3083	0.0696	-0.7713	-0.221	-0.048	-0.0067	-0.0816	-0.1253	-0.0332	-0.0996	-2.3865	21.9807	-2.2213
10	0.0156	-3.7598	-9.3563	8.1623	-7.1031	2.6551	-0.1651	0.6911	-0.1676	-0.5314	0.3991	-0.6376	-0.6543	0.9967	-0.2339	0.0051	-0.0964	-0.0109	0.2332	-0.0263	-0.0025	6.8031	27.7896	-8.3632
11	1.7099	0.7691	0.9185	1.4359	1.1785	1.3393	0.1489	-0.1701	-0.1321	0.0921	-0.1489	0.0991	0.0093	-0.2859	0	-0.1346	-0.0054	-0.0071	-0.1018	0.0019	-0.1716	-0.2439	29.0392	9.5236
12	3.7283	-4.2698	6.7668	10.1486	0.5127	8.1989	-0.0189	-0.0537	0.514	0.3635	0.1291	-0.7395	-0.0654	0.721	-0.1101	-0.1289	-0.127	-0.0883	0.0182	0.0063	-0.1696	22.6695	35.2107	26.8901
13	0.1294	-0.8845	-0.9085	3.2894	0.3207	3.7266	-0.1229	-0.1509	0.2354	0.3986	0.1212	-0.606	-0.5364	0.7351	0.0017	0.0715	-0.1397	-0.1654	0.0781	0.0195	-0.0049	19.0473	36.4738	23.6228
14	6.8229	12.0649	0.4961	0.2456	-3.7467	0.7457	0.1123	0.1732	-0.8515	-0.0702	-0.0463	1.1406	0.5236	0.0864	-0.066	0.243	-0.0946	0.0292	0.1002	-0.0946	0.7104	-8.173	18.0292	14.5576
15	3.187	1.568	2.1995	0.5955	2.5983	0.0034	-0.1043	-0.5299	-0.62	0.2091	0.1288	0.9556	0.4018	-0.1174	-0.0245	0.0098	-0.0417	0.1134	-0.044	0.0531	0.2483	-3.8849	19.1521	18.5598
16	1.2558	0.4781	-0.9261	2.9097	-1.3116	2.0784	0.1138	-0.0573	-0.1259	0.1702	-0.0844	-0.105	-0.1525	0.0674	-0.0294	-0.0855	-0.0517	-0.0382	-0.0679	-0.0041	-0.1633	12.4206	33.5669	10.1965
17	13.474	5.0871	-5.5823	6.5396	7.2525	8.6329	0.3669	0.3906	0.4711	0.2715	-0.5234	1.324	-0.7731	-0.6099	0.1565	0.0835	0.0316	0.1241	-0.179	-0.0097	-0.0361	4.4942	48.7248	14.9502
18	2.609	1.1741	-1.3807	3.7548	-2.7589	4.4695	0.2583	-0.1344	0.3338	-0.0065	-0.1619	0.0468	-0.3272	-0.0541	-0.0964	-0.0229	-0.0564	0.019	-0.1883	-0.0283	-0.1853	9.0535	46.2671	16.89
19	0	0.3035	0.6465	6.3533	-1.5486	5.2551	0.0754	-0.526	0.0891	0.9873	-0.1197	-0.1419	-0.1966	0.3229	0.0443	-0.026	-0.1137	-0.0228	-0.0352	0.0302	-0.2284	9.4855	30.4315	28.891
20	4.9068	-9.4157	-0.0038	2.7252	4.0358	1.0844	-0.0576	0.1055	-0.4698	-0.0649	-0.0592	-0.7096	0.238	0.6091	0.1167	0.1444	-0.0212	-0.1183	0.2235	0.0469	0.2151	27.3754	24.4311	27.2283
21	2.5026	0.4633	-1.6627	1.0561	-2.2471	0.0225	0.065	0.2299	0.0282	-0.1086	-0.0573	0.0336	0.0832	-0.1847	-0.0078	0.0649	-0.2476	-0.1708	0.1269	0.3394	0.3415	-19.4589	-2.2323	0.5141
22	7.9484	5.8962	-4.5574	7.6903	-1.9488	0	0.071	-0.6357	1.9635	-0.1371	-0.0943	1.481	-0.4407	-0.9886	0.0233	-0.3549	-0.0652	0.1731	-0.5467	-0.2154	0.1406	-10.7486	3.3016	17.134
23	10.445	-16.7844	-5.4113	6.4578	-6.3987	7.7622	0.0371	-0.414	0.5446	0.2247	0.1245	-0.1218	-0.3671	-0.1811	-0.1616	0.1562	-0.7109	0.3354	0.1915	-0.3213	-0.0469	-10.2259	-1.9715	28.5372
24	7.7852	-0.9949	-5.4023	0	7.1946	10.1681	0.393	-1.5015	-0.8665	1.0494	-0.6603	-0.6609	1.3911	0.164	0.2674	0.561	-0.3815	0.0315	-0.0613	0.2295	0.0216	3.6258	-6.2767	29.2424
25	4.9159	6.7332	1.9596	5.6245	2.6615	4.3834	0.3381	0.1586	-0.9217	0.4409	0.0373	-1.0797	1.0107	0.3652	-0.3754	-0.0831	0.0586	0.0345	-0.3634	0.0063	0.0084	8.0089	-2.9821	18.8805
26	4.3367	3.8357	3.5814	7.4193	-4.7546	9.7705	-0.3935	0.5775	0.5014	-1.2612	0.2985	0.2533	-0.4401	0.1215	0.0949	-0.0013	-0.1445	0.0685	-0.1977	0.0008	-0.0573	2.056	5.1554	7.5861
27	2.8617	2.4205	6.7952	1.0216	-0.4854	9.9226	-0.3022	0.7055	-0.3068	-1.0429	0.1625	-0.4606	0.1401	0.1126	0.1397	0.0718	-0.1416	0.1673	-0.0404	-0.0258	-0.0945	9.9388	6.9951	7.83
28	5.0282	2.6347	-0.3634	9.3177	-2.3104	0.6885	0.0332	0.1783	0.0512	0.1352	0.2571	-0.1427	-0.2366	0.5744	-0.2904	-0.2594	-0.023	0.0605	-0.2926	0.0662	-0.0565	12.8418	10.3488	19.7468
29	0.001	-3.4585	8.8471	0.8138	-9.0905	3.2015	0.0719	-0.083	-0.8143	0.1934	0.1566	-0.3685	0.4319	0.5086	-0.2285	-0.233	-0.0033	0.1193	-0.022	-0.1135	0.3818	22.8581	3.2246	20.3999
30	0.0123	-12.0205	-1.9756	0	-1.3107	0	-0.0032	0.2572	-0.6781	0.1456	0.1055	-0.4425	0.5658	0.395	-0.1023	0.0122	0.1727	0.0768	0.0307	-0.1049	0.5312	21.1638	-2.3458	16.1972
31	7.2215	6.8155	0.7707	7.2444	1.7461	6.4497	0.4772	-0.9938	0.2905	0.9018	-0.8862	0.1945	0.3326	0.0426	0.409	-0.1656	-0.1044	0.1513	-0.3919	-0.0106	-0.181	3.9366	3.1357	24.1347
32	2.6746	6.3662	4.5894	3.4402	5.2493	14.6527	-0.0619	0.0221	0.383	-0.0736	0.027	0.2188	-0.037	-0.5082	0.0349	-0.1364	-0.119	-0.0988	-0.3487	0.1363	0.2732	-14.0448	-2.0727	7.4184
33	1.9891	1.213	3.7072	0.1244	-1.6855	0.5357	-0.0206	0.2835	-0.0338	-0.1489	0.0481	0.1177	0.0286	-0.2231	-0.0276	0.5022	-0.3353	-0.2652	0.688	0.0616	0.7828	-25.6376	-7.7847	4.6917
34	0.0274	2.1143	3.9443	0.0527	0.3588	0	-0.0522	0.0576	-0.0203	-0.1157	0.2009	0.1613	0.1977	-0.0543	-0.1487	-0.0588	-0.1156	-0.145	-0.3603	0.0416	0.1851	-12.1435	-5.9224	8.9788
35	0	5.4988	2.0682	11.6622	2.4344	1.0678	-0.066	-0.1279	0.0908	0.7653	-0.3412	0.8084	0.1121	0.0872	0.4072	-0.1438	-0.0447	0.0785	-0.2385	-0.063	0.0053	2.6962	12.4772	22.8655
36	0.9369	8.1733	5.6169	7.2035	1.5059	4.0462	0.1043	-0.0185	0.4968	-0.1141	-0.4339	0.8481	-0.2271	-0.2334	0.3296	-0.1149	-0.0702	0.1265	-0.2829	-0.0675	0.0269	0.5189	8.182	16.8883
37	10.3539	9.1981	-2.9589	10.025	2.153	4.5819	0.2808	-0.1721	-0.6576	-0.202	-0.0614	-1.1468	0.3824	0.4307	-0.2194	-0.1511	-0.0287	0.132	-0.3704	-0.0579	0.0239	1.0349	-11.2595	14.4112
38	0	-2.0134	-3.5399	3.5348	9.8512	8.5374	0.0839	-0.8172	0.4165	1.2992	-0.1381	0.1249	0.0044	0.8678	0.0542	0.2916	-0.2289	-0.065	0.1236	-0.0033	-0.0158	-8.9008	-17.1622	27.8743
39	0.8861	4.6438	-0.8817	7.3351	5.3349	0	0.6831	-0.5494	0.1648	0.304	-0.6692	-0.3106	-0.2869	0.1462	-0.014	-0.058	-0.1511	0.0872	-0.2674	-0.0062	-0.1441	-7.7975	-12.053	18.3053
40	0.7446	-4.0942	0.4097	13.1754	-0.6665	2.4011	-0.0352	0.0823	0.8023	-0.467	-0.2018	0.7121	-0.2453	-0.7433	0.237	-0.1183	-0.151	0.2102	-0.1751	-0.2098	0.6032	-14.3143	3.8697	14.881

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|66 - A\|76 }	A	66 - 76
2	X-RAY DIFFRACTION	2	{ A\|77 - A\|82 }	A	77 - 82
3	X-RAY DIFFRACTION	3	{ A\|83 - A\|92 }	A	83 - 92
4	X-RAY DIFFRACTION	4	{ A\|93 - A\|97 }	A	93 - 97
5	X-RAY DIFFRACTION	5	{ A\|98 - A\|109 }	A	98 - 109
6	X-RAY DIFFRACTION	6	{ A\|110 - A\|124 }	A	110 - 124
7	X-RAY DIFFRACTION	7	{ A\|125 - A\|132 }	A	125 - 132
8	X-RAY DIFFRACTION	8	{ A\|133 - A\|138 }	A	133 - 138
9	X-RAY DIFFRACTION	9	{ A\|139 - A\|147 }	A	139 - 147
10	X-RAY DIFFRACTION	10	{ A\|148 - A\|153 }	A	148 - 153
11	X-RAY DIFFRACTION	11	{ A\|154 - A\|172 }	A	154 - 172
12	X-RAY DIFFRACTION	12	{ A\|173 - A\|178 }	A	173 - 178
13	X-RAY DIFFRACTION	13	{ A\|179 - A\|194 }	A	179 - 194
14	X-RAY DIFFRACTION	14	{ A\|195 - A\|202 }	A	195 - 202
15	X-RAY DIFFRACTION	15	{ A\|203 - A\|207 }	A	203 - 207
16	X-RAY DIFFRACTION	16	{ A\|208 - A\|223 }	A	208 - 223
17	X-RAY DIFFRACTION	17	{ A\|224 - A\|231 }	A	224 - 231
18	X-RAY DIFFRACTION	18	{ A\|232 - A\|248 }	A	232 - 248
19	X-RAY DIFFRACTION	19	{ A\|249 - A\|255 }	A	249 - 255
20	X-RAY DIFFRACTION	20	{ A\|256 - A\|260 }	A	256 - 260
21	X-RAY DIFFRACTION	21	{ B\|68 - B\|70 }	B	68 - 70
22	X-RAY DIFFRACTION	22	{ B\|71 - B\|78 }	B	71 - 78
23	X-RAY DIFFRACTION	23	{ B\|79 - B\|83 }	B	79 - 83
24	X-RAY DIFFRACTION	24	{ B\|84 - B\|97 }	B	84 - 97
25	X-RAY DIFFRACTION	25	{ B\|98 - B\|109 }	B	98 - 109
26	X-RAY DIFFRACTION	26	{ B\|110 - B\|124 }	B	110 - 124
27	X-RAY DIFFRACTION	27	{ B\|125 - B\|135 }	B	125 - 135
28	X-RAY DIFFRACTION	28	{ B\|136 - B\|142 }	B	136 - 142
29	X-RAY DIFFRACTION	29	{ B\|143 - B\|147 }	B	143 - 147
30	X-RAY DIFFRACTION	30	{ B\|148 - B\|155 }	B	148 - 155
31	X-RAY DIFFRACTION	31	{ B\|156 - B\|171 }	B	156 - 171
32	X-RAY DIFFRACTION	32	{ B\|172 - B\|176 }	B	172 - 176
33	X-RAY DIFFRACTION	33	{ B\|177 - B\|184 }	B	177 - 184
34	X-RAY DIFFRACTION	34	{ B\|185 - B\|189 }	B	185 - 189
35	X-RAY DIFFRACTION	35	{ B\|190 - B\|203 }	B	190 - 203
36	X-RAY DIFFRACTION	36	{ B\|204 - B\|213 }	B	204 - 213
37	X-RAY DIFFRACTION	37	{ B\|214 - B\|226 }	B	214 - 226
38	X-RAY DIFFRACTION	38	{ B\|227 - B\|235 }	B	227 - 235
39	X-RAY DIFFRACTION	39	{ B\|236 - B\|247 }	B	236 - 247
40	X-RAY DIFFRACTION	40	{ B\|248 - B\|256 }	B	248 - 256

-
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