PDB-3ivl: The Crystal Structure of the Inactive Peptidase Domain of a Putat...

ID or keywords:

Entry

Database: PDB / ID: 3ivl

Title

The Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from Bordetella parapertussis to 2.2A

Components

Putative zinc protease

Keywords

HYDROLASE / protease / inactive / peptidase / bordetella / parapertussis / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative

Function / homology

Function and homology information

metalloendopeptidase activity / metal ion binding
Similarity search - Function

Biological species

Bordetella parapertussis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.2 Å

Authors

Stein, A.J. / Wu, R. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from Bordetella parapertussis to 2.2A
Authors: Stein, A.J. / Wu, R. / Keigher, L. / Joachimiak, A.

History

Deposition	Sep 1, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3ivl.cif.gz	83.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3ivl.ent.gz	69.3 KB	Display	PDB format
PDBx/mmJSON format	3ivl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3ivl_validation.pdf.gz	459.7 KB	Display	wwPDB validaton report
Full document	3ivl_full_validation.pdf.gz	471 KB	Display
Data in XML	3ivl_validation.xml.gz	16.9 KB	Display
Data in CIF	3ivl_validation.cif.gz	22.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/3ivl ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3ivl	HTTPS FTP

-
Related structure data

Similar structure data	5h66-d 5tuu-2 3d55-2 2pso-d 3vf0-1 3t7i-d 5h67-d 3oxq-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
Other databases	TargetDB: APC36318.1

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#36 - Dec 2002 Cytochrome c similarity (7) #137 - May 2011 Cytochrome bc1 similarity (5)

Deposited unit

A: Putative zinc protease

B: Putative zinc protease

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: Putative zinc protease

hetero molecules

A: Putative zinc protease

hetero molecules

A: Putative zinc protease

hetero molecules

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

3

B: Putative zinc protease

hetero molecules

B: Putative zinc protease

hetero molecules

B: Putative zinc protease

hetero molecules

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

Unit cell

Length a, b, c (Å)	108.173, 108.173, 113.995
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Details

authors state that biological unit is the same as asymmetric unit.

#1: Protein	Putative zinc protease Mass: 22930.289 Da / Num. of mol.: 2 / Fragment: residues 258-465, Inactive Peptidase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella parapertussis (bacteria) / Gene: BPP3483 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7W521
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.5 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion / pH: 6.5 Details: 40% PEG 300, 0.1M Sodium cacodylate pH 6.5, 0.2M Calcium acetate, vapor diffusion, temperature 297K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2009

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 28929 / % possible obs: 99.6 % / Redundancy: 4.4 % / R_merge(I) obs: 0.099 / Χ²: 2.809 / Net I/σ(I): 10.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.1-2.18	4.4	0.72	2896	1.131	1	100
2.18-2.26	4.4	0.479	2913	1.294	1	100
2.26-2.37	4.4	0.432	2898	1.209	1	100
2.37-2.49	4.4	0.269	2914	1.337	1	100
2.49-2.65	4.4	0.195	2888	1.408	1	100
2.65-2.85	4.4	0.134	2912	1.679	1	100
2.85-3.14	4.4	0.098	2898	2.219	1	99.9
3.14-3.59	4.4	0.08	2905	3.578	1	100
3.59-4.52	4.3	0.07	2909	5.623	1	99.8
4.52-50	4.3	0.07	2796	9.141	1	96.3

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.5.0102	refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 2.2→43.33 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.925 / WR_factor R_free: 0.253 / WR_factor R_work: 0.213 / SU B: 14.902 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.258	1273	5.1 %	RANDOM
R_work	0.216	-	-	-
obs	0.219	25100	99.53 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	-0.03 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	0.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→43.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2752	0	14	51	2817

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	2833
X-RAY DIFFRACTION	r_angle_refined_deg	1.442	1.981	3863
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.628	5	371
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.865	22.477	109
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.877	15	419
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.679	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	449
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2151
X-RAY DIFFRACTION	r_mcbond_it	0.518	1.5	1850
X-RAY DIFFRACTION	r_mcangle_it	0.936	2	2934
X-RAY DIFFRACTION	r_scbond_it	1.84	3	983
X-RAY DIFFRACTION	r_scangle_it	2.712	4.5	927

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.201-2.258	0.333	98	0.328	1738	1837	99.946
2.258-2.32	0.325	92	0.297	1720	1813	99.945
2.32-2.387	0.32	111	0.274	1675	1786	100
2.387-2.46	0.263	82	0.246	1644	1726	100
2.46-2.54	0.325	102	0.25	1554	1656	100
2.54-2.629	0.245	73	0.243	1519	1593	99.937
2.629-2.728	0.333	69	0.242	1504	1573	100
2.728-2.839	0.253	66	0.227	1423	1489	100
2.839-2.965	0.227	79	0.229	1353	1433	99.93
2.965-3.109	0.279	59	0.226	1282	1342	99.925
3.109-3.276	0.242	76	0.213	1257	1333	100
3.276-3.473	0.23	61	0.209	1157	1219	99.918
3.473-3.711	0.291	43	0.216	1118	1161	100
3.711-4.006	0.245	68	0.187	1010	1079	99.907
4.006-4.385	0.24	50	0.181	923	977	99.591
4.385-4.896	0.234	34	0.162	874	915	99.235
4.896-5.642	0.207	44	0.198	751	801	99.251
5.642-6.881	0.199	24	0.223	630	658	99.392
6.881-9.61	0.218	30	0.182	469	523	95.411
9.61-43.325	0.462	12	0.266	226	305	78.033

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	1.4217	-3.1434	-2.8505	7.8127	6.6029	5.9411	-0.0946	-0.0601	0.0451	-0.1148	0.2532	-0.3363	-0.029	0.1344	-0.1586	0.203	-0.0163	0.0254	0.1446	-0.0441	0.2564	9.1434	30.7175	1.4669
2	2.5595	3.5016	-2.8945	23.9088	19.8434	33.4966	-0.0303	0.4278	-0.0595	-0.5011	0.0191	-0.0661	-0.38	-1.048	0.0112	0.1686	0.0199	0.1079	0.1722	0.029	0.3187	19.2097	9.743	-10.1681
3	42.9618	27.184	8.4787	21.6854	15.671	25.4474	0.5117	-0.2211	-1.9866	0.7877	0.0575	-1.3528	1.3367	0.3274	-0.5692	0.5072	-0.0054	0.0049	0.2041	-0.0372	0.3888	21.3781	-3.7361	-10.4544
4	13.9281	-1.5912	-3.8887	15.1081	3.8847	1.9956	-0.1749	-0.2148	0.2048	0.1489	0.1876	-0.0335	0.0793	-0.0647	-0.0128	0.2104	-0.0332	-0.0729	0.2478	-0.0033	0.1183	21.0881	3.1802	0.1398
5	9.9746	-5.3623	-2.8951	12.7763	11.1037	10.2755	-0.1189	-1.4462	0.122	0.372	0.4235	-0.5039	-0.0385	0.1113	-0.3045	0.6627	-0.1283	-0.2463	0.3773	-0.1065	0.5269	21.8441	17.5841	7.9397
6	9.6557	-7.4728	-8.6601	16.0879	11.1856	10.8586	0.1504	-0.6112	0.2903	0.2673	-0.0659	-0.381	-0.2879	0.2757	-0.0845	0.3534	-0.0616	0.0006	0.2291	-0.04	0.1622	14.5672	12.4632	1.2089
7	20.6354	5.9193	9.9923	5.4149	3.6032	5.0523	0.2074	-0.8195	-0.1366	-0.603	-0.3495	1.1519	0.0559	-0.4927	0.1421	0.5436	-0.2056	0.0256	0.4177	-0.0791	0.5747	12.9102	4.9464	-9.9368
8	10.8965	-10.9141	-2.2411	45.0494	10.7279	3.0443	0.4758	-0.1406	1.3241	0.8109	-0.3017	-1.1152	0.074	-0.1903	-0.174	0.2839	0.0002	0.0224	0.2223	-0.0662	0.2768	14.7314	21.7632	1.8868
9	54.8689	-2.264	-8.4151	20.7717	4.2242	2.0572	0.4143	-0.5229	1.042	0.3517	-0.029	-1.2443	-0.0545	0.1118	-0.3853	0.5563	0.0183	0.2379	0.1097	-0.1226	0.7987	19.2052	28.6614	-1.2979
10	10.3712	-5.3524	-1.2477	3.6756	-0.1566	2.4807	0.1988	0.042	-0.2172	0.1431	-0.1453	-0.5844	-0.1333	0.4002	-0.0535	0.3685	-0.1541	-0.1037	0.2682	-0.0908	0.8886	27.6667	15.8134	-2.4534
11	18.8746	0.5164	-6.9671	11.1971	-3.9241	13.2163	-0.3812	-1.7939	0.6403	1.3366	0.2316	-1.3819	-0.2351	1.117	0.1495	0.3008	0.0239	-0.2125	0.4517	-0.1921	0.3502	27.8749	1.452	7.4194
12	12.7513	7.6719	3.4431	9.3715	0.4177	4.3152	0.2861	-1.0592	0.0472	0.8196	-0.3953	0.5164	-0.4921	-0.4227	0.1092	0.5441	0.1464	0.0896	0.1672	0.017	0.0959	13.5947	-6.1149	5.8186
13	6.9601	-1.8277	3.3017	9.2128	2.0924	31.0664	-0.0527	-0.4655	-0.2359	-0.4287	-0.2202	1.2949	-0.9528	-1.0726	0.2729	0.1825	0.0255	-0.0258	0.2049	-0.0271	0.428	3.8269	-8.879	-3.6539
14	12.6905	5.3068	7.3617	6.1861	4.0205	4.6745	-0.1306	0.6358	-0.3819	-0.0993	0.1707	-0.179	-0.1727	0.264	-0.0401	0.2016	0.031	-0.0014	0.1794	-0.0225	0.2072	17.2903	-11.5258	-3.4079
15	2.0868	-2.1982	2.6237	5.544	-4.8555	7.1481	0.436	-0.1168	0.2315	-0.7965	-0.3072	-1.0761	0.4486	0.2322	-0.1288	0.2447	-0.0291	0.2169	0.2177	0.0388	0.6296	28.6629	5.0848	-6.9847
16	20.4083	-9.9771	-7.6475	6.3571	3.6051	8.5002	0.1077	0.4871	1.8945	-0.2809	-0.2788	-1.1822	-0.8324	-0.6029	0.1711	0.3028	0.0457	0.0071	0.1111	-0.0423	0.3994	12.7893	23.8942	-7.6925
17	0.7111	2.1179	3.8112	47.9177	21.7575	26.3198	-0.036	0.2868	-0.22	-1.9218	-0.064	1.5021	-0.2104	1.0348	0.1001	0.4201	0.1764	0.1064	0.3611	-0.0324	0.5069	0.5078	42.1501	0.1363
18	8.4173	-1.4962	6.4549	0.3785	-1.2278	6.1422	-0.0553	0.5523	-0.0351	0.0892	-0.1519	-0.1908	-0.0311	0.8603	0.2072	0.2507	-0.0091	-0.1032	0.2247	0.0807	0.3892	75.3494	6.9292	-17.8516
19	6.5878	-7.507	0.1182	11.1113	-0.2103	5.8279	-0.0051	0.1975	0.2548	0.2858	-0.0461	0.3042	-0.5675	-0.3523	0.0512	0.1724	0.006	0.0286	0.1969	0.0852	0.1633	44.0633	13.4089	-27.8989
20	9.1355	-3.4656	4.1241	9.5511	0.1157	2.4005	0.2525	-0.2366	-0.0163	0.7887	-0.1133	0.0754	0.0655	-0.0781	-0.1392	0.4531	0.0331	0.2097	0.3285	0.0405	0.1351	45.5579	11.2464	-17.6395
21	6.6011	-1.9427	6.7799	12.1965	-4.3679	7.6384	-0.1406	-1.6582	0.5251	0.9759	-0.2416	0.4345	-0.5288	-1.5091	0.3822	0.6912	0.0262	0.0656	0.6019	-0.0468	0.2377	52.5505	6.9276	-10.1692
22	2.8867	-2.1126	3.0014	13.7658	-1.9654	7.9633	0.0577	-0.5112	-0.0798	0.8498	-0.0202	-0.2702	0.1838	0.4866	-0.0375	0.3937	-0.0068	-0.0347	0.3613	0.0787	0.0582	60.1167	4.138	-12.6079
23	6.1074	3.4291	1.2595	9.4144	-4.1141	10.04	0.0134	0.2505	0.573	0.3143	-0.0686	-0.0466	-0.8677	-0.1395	0.0553	0.2683	0.0729	0.0336	0.2252	-0.0207	0.189	50.9895	17.9341	-27.0887
24	20.0621	6.7111	4.0163	3.3819	0.766	2.4756	0.1422	0.0133	-0.8296	0.2414	0.0255	-0.5244	0.0024	0.4009	-0.1677	0.3198	0.0095	-0.1117	0.2057	0.0404	0.1979	63.5711	7.726	-17.7082
25	53.122	14.7457	13.1475	10.2594	-2.4245	9.4697	-0.2821	1.9177	-3.2155	0.2174	0.608	-1.5111	-0.2282	0.6166	-0.326	0.3016	0.0878	-0.026	0.272	-0.2151	0.5822	67.0218	-0.473	-20.1891
26	35.8471	4.4711	3.2379	25.7895	-3.8577	8.8418	-0.3061	-0.207	-1.2399	-0.1004	0.3302	0.4752	-0.3283	0.0144	-0.0242	0.3569	0.0289	0.0309	0.1954	0.0193	0.066	57.3629	0.2994	-21.5238
27	17.1938	3.0586	-6.1156	3.0385	-2.483	4.9427	-0.3275	0.0696	-0.9028	0.3705	0.2996	0.4552	0.5454	-0.2614	0.0279	0.3128	0.0465	0.1251	0.1325	0.0782	0.3838	46.1307	-0.7527	-19.8268
28	1.1547	-2.3703	-3.5605	13.4866	8.574	12.7813	-0.1159	-0.2532	-0.3789	1.0406	-0.6855	0.5652	0.4955	-0.2972	0.8013	0.3625	0.0209	0.1183	0.7722	0.3303	0.2562	39.917	8.3296	-10.4268
29	0.1399	0.5474	-0.0634	18.6322	-2.6768	0.4141	-0.029	-0.2248	0.0305	1.3174	0.06	0.3263	-0.1154	-0.0422	-0.031	0.3751	0.1144	0.0564	0.4304	-0.0044	0.1042	40.8184	22.8493	-12.819
30	6.8654	-1.217	1.4591	3.165	-0.4455	15.6687	-0.0183	-0.1311	0.3212	0.3714	0.0643	-0.4979	0.2145	1.0305	-0.0461	0.2335	0.0667	0.0103	0.224	0.0069	0.2513	43.2128	32.4566	-22.2025
31	6.2015	-1.6494	-0.6254	10.0214	-4.8628	5.7564	-0.3098	-0.2179	-0.0822	-0.4904	0.1028	0.239	0.512	0.2792	0.2071	0.1778	0.0493	0.0391	0.1827	0.0048	0.237	35.354	25.8543	-22.9699
32	6.4295	-2.0812	-4.4365	0.9996	1.9872	6.5241	-0.2348	0.334	-0.1781	0.2778	-0.0269	0.336	0.153	-0.4576	0.2617	0.2483	0.0525	0.132	0.1902	0.066	0.4336	37.7663	8.5737	-21.6731
33	1.0153	1.5394	-0.8477	6.3402	1.1233	2.5016	0.1485	0.0141	-0.1742	0.3036	-0.1079	-0.3872	-0.0881	0.1444	-0.0406	0.1895	0.0193	0.0013	0.2035	-0.0163	0.1245	59.3342	4.8511	-29.2555
34	24.9681	-1.6112	12.443	0.3528	-0.7476	6.3858	-0.0332	1.3551	0.0394	-0.2237	-0.0245	0.3106	-0.1241	0.3794	0.0576	0.3273	0.0492	-0.1316	0.6327	0.1525	0.5923	85.2128	6.6714	-20.3477

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	270 - 282
2	X-RAY DIFFRACTION	2	A	283 - 287
3	X-RAY DIFFRACTION	3	A	288 - 294
4	X-RAY DIFFRACTION	4	A	295 - 307
5	X-RAY DIFFRACTION	5	A	308 - 323
6	X-RAY DIFFRACTION	6	A	324 - 330
7	X-RAY DIFFRACTION	7	A	331 - 340
8	X-RAY DIFFRACTION	8	A	341 - 347
9	X-RAY DIFFRACTION	9	A	348 - 353
10	X-RAY DIFFRACTION	10	A	354 - 368
11	X-RAY DIFFRACTION	11	A	369 - 377
12	X-RAY DIFFRACTION	12	A	378 - 390
13	X-RAY DIFFRACTION	13	A	391 - 406
14	X-RAY DIFFRACTION	14	A	407 - 423
15	X-RAY DIFFRACTION	15	A	424 - 439
16	X-RAY DIFFRACTION	16	A	440 - 449
17	X-RAY DIFFRACTION	17	A	450 - 456
18	X-RAY DIFFRACTION	18	B	270 - 282
19	X-RAY DIFFRACTION	19	B	283 - 297
20	X-RAY DIFFRACTION	20	B	298 - 306
21	X-RAY DIFFRACTION	21	B	307 - 314
22	X-RAY DIFFRACTION	22	B	315 - 328
23	X-RAY DIFFRACTION	23	B	329 - 340
24	X-RAY DIFFRACTION	24	B	341 - 347
25	X-RAY DIFFRACTION	25	B	348 - 353
26	X-RAY DIFFRACTION	26	B	354 - 360
27	X-RAY DIFFRACTION	27	B	361 - 369
28	X-RAY DIFFRACTION	28	B	370 - 378
29	X-RAY DIFFRACTION	29	B	379 - 389
30	X-RAY DIFFRACTION	30	B	390 - 408
31	X-RAY DIFFRACTION	31	B	409 - 418
32	X-RAY DIFFRACTION	32	B	419 - 436
33	X-RAY DIFFRACTION	33	B	437 - 446
34	X-RAY DIFFRACTION	34	B	447 - 456

-
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://pdbjlvh1.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