PDB-3lrd: Self-assembly of spider silk proteins is controlled by a pH-sensi...

ID or keywords:

Entry

Database: PDB / ID: 3lrd

Title

Self-assembly of spider silk proteins is controlled by a pH-sensitive relay

Components

Major ampullate spidroin 1

Keywords

STRUCTURAL PROTEIN / dragline spider silk / self-assembly / pH-dependence / NT D40N/E84Q double-mutant

Function / homology

Function and homology information

identical protein binding
Similarity search - Function

Biological species

Euprosthenops australis (spider)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Askarieh, G. / Hedhammar, H. / Nordling, K. / Rising, A. / Johansson, J. / Knight, S.D. / Saenz, A. / Casals, C.

Citation

Journal: Nature / Year: 2010
Title: Self-assembly of spider silk proteins is controlled by a pH-sensitive relay.
Authors: Askarieh, G. / Hedhammar, M. / Nordling, K. / Saenz, A. / Casals, C. / Rising, A. / Johansson, J. / Knight, S.D.

History

Deposition	Feb 11, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 12, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 13, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3lrd.cif.gz	107.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3lrd.ent.gz	87.1 KB	Display	PDB format
PDBx/mmJSON format	3lrd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3lrd_validation.pdf.gz	455.8 KB	Display	wwPDB validaton report
Full document	3lrd_full_validation.pdf.gz	457.4 KB	Display
Data in XML	3lrd_validation.xml.gz	11.9 KB	Display
Data in CIF	3lrd_validation.cif.gz	15.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lr/3lrd ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lrd	HTTPS FTP

-
Related structure data

Related structure data	3lr2C 3lr6C 3lr8C C: citing same article (ref.)
Similar structure data	1sfi-d 3f9o-d 4gaw-12 1x8h-d 3lr2-d 2fuk-d 1sbw-d 1olr-d 6r9d-1 5eg4-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Major ampullate spidroin 1

B: Major ampullate spidroin 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	68.383, 68.383, 97.781
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	B-155- HOH
2	1	B-175- HOH

#1: Protein	Major ampullate spidroin 1 Mass: 14181.743 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: D40N, E84Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Euprosthenops australis (spider) / Gene: MaSp1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05H60
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.14 %
Crystal grow	Method: vapor diffusion / Details: Ammonium sulphate, PEG 400, VAPOR DIFFUSION

-
Data collection

Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
Detector	Type: ADSC QUANTUM 315 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.06→59.23 Å / Num. obs: 14086 / Observed criterion σ(I): 1.8 / Redundancy: 5.3 % / R_merge(I) obs: 0.087 / Net I/σ(I): 7.2
Reflection shell	Resolution: 2.06→2.206 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.421 / Mean I/σ(I) obs: 4 / Num. unique all: 2416

-
Processing

Software

Name: REFMAC / Version: 5.2.0019 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NT wild-type

Resolution: 2.15→59.2 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.913 / SU B: 9.362 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22841	739	5 %	RANDOM
R_work	0.17013	-	-	-
obs	0.17299	14086	99.52 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 14.606 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.78 Å²	0.39 Å²	0 Å²
2-	-	0.78 Å²	0 Å²
3-	-	-	-1.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→59.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1856	0	18	55	1929

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1933
X-RAY DIFFRACTION	r_angle_refined_deg	1.423	1.943	2619
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.894	5	269
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.986	27.123	73
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.628	15	320
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.151	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	302
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1450
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	924
X-RAY DIFFRACTION	r_nbtor_refined	0.295	0.2	1389
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	67
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.194	0.2	35
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.162	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.889	1.5	1326
X-RAY DIFFRACTION	r_mcangle_it	1.133	2	2074
X-RAY DIFFRACTION	r_scbond_it	2.236	3	674
X-RAY DIFFRACTION	r_scangle_it	3.016	4.5	540

LS refinement shell

Resolution: 2.15→2.206 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.238	59	-
R_work	0.161	1037	-
obs	-	-	99.73 %

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	23.8146	-5.1815	2.1857	24.0284	-6.7344	28.6759	-0.421	-0.467	0.479	-0.0467	-0.5039	-2.0058	0.2574	2.0489	0.9248	0.0658	-0.0253	-0.0316	0.1915	0.0998	0.2308	-13.213	20.7298	16.9536
2	9.1728	-5.3798	0.1665	13.7135	3.4235	7.0058	-0.1457	0.1805	0.0402	0.1918	-0.2935	-0.213	0.4223	-0.3519	0.4392	0.0836	-0.0763	-0.0087	0.0694	-0.0003	-0.0009	-22.3297	18.4488	17.1607
3	6.9593	-6.4143	5.5409	15.9052	-2.8966	4.9006	-0.1257	-0.3067	-0.2304	0.2053	-0.0962	-0.0712	-0.1695	-0.6633	0.2219	0.0364	-0.0407	-0.0224	0.131	-0.0434	0.0455	-25.3431	26.3364	19.3487
4	2.7057	-8.1332	-3.6711	28.6267	0.4315	31.8916	0.2885	-0.6578	-0.0293	-0.1749	0.489	1.2137	-0.2379	-0.7195	-0.7774	0.1662	0.0193	-0.0394	0.1492	-0.027	0.0938	-27.8883	34.2613	20.5755
5	18.3784	7.1298	3.9403	9.5991	-2.9039	3.72	-0.1877	-1.0144	-0.0816	0.5213	-0.1711	-0.0699	-0.4242	-0.3627	0.3588	0.2141	0.1009	-0.0441	0.0408	-0.1086	0.1152	-29.9885	42.8321	18.3943
6	5.7829	-5.9294	2.7628	21.142	4.5373	7.2775	-0.0546	-0.3609	0.0324	0.3421	0.2746	0.2878	-0.3953	-0.2179	-0.2199	0.0897	0.063	0.0402	0.0517	-0.0389	0.026	-33.2903	35.3415	12.9133
7	8.8062	-7.8269	7.0022	50.8484	-5.7355	5.5731	-0.512	0.1607	0.0109	-0.0623	0.2146	1.2887	-0.4436	-0.792	0.2974	0.0902	0.0163	0.013	0.1496	0.0322	0.0572	-32.4735	23.8174	11.7162
8	7.961	-0.0452	5.8738	15.2251	9.6943	10.5492	-0.1963	0.1175	-0.2427	0.3141	-0.0488	0.0671	-0.0815	-0.6301	0.2451	0.1341	-0.0423	0.0898	0.0728	0.0358	0.0093	-29.7222	15.3608	11.0047
9	1.4439	3.781	-1.7908	13.7808	-1.5349	4.7859	0.1627	0.1242	-0.2216	-0.0119	-0.046	-0.0637	0.2813	0.0626	-0.1167	0.1966	0.0048	0.0194	0.0898	0.0172	0.135	-23.9023	12.6372	7.6623
10	4.9039	0.0528	1.8295	17.4936	3.4454	7.5082	0.3405	0.5389	-0.0383	-0.4481	-0.4628	-0.3841	-0.0316	0.3619	0.1223	0.1031	-0.0226	0.0015	0.1224	-0.0129	0.0176	-19.3479	20.3395	7.445
11	6.618	-1.9088	-0.621	34.9657	0.4917	0.0611	-0.0442	-0.3051	0.4807	0.5232	-0.3984	-0.1521	-0.0674	0.6174	0.4427	0.1941	-0.015	0.0105	0.1521	-0.006	0.0375	-22.4222	29.339	9.3506
12	7.6077	-4.5319	-1.6134	2.8955	0.5663	1.1381	0.1068	-0.1383	0.0166	0.2313	-0.5831	-0.2326	-0.2263	-0.4541	0.4763	0.2278	-0.0444	-0.0288	0.1146	-0.0678	0.095	-26.4568	37.6038	8.3446
13	6.7602	6.3074	-3.046	7.179	-3.4294	1.6391	-0.1197	0.3904	0.3463	0.1156	-0.0488	-0.0356	-0.0291	-0.3842	0.1685	0.336	0.0211	-0.0589	0.0843	-0.0112	0.2552	-28.9547	46.6795	9.4152
14	2.5686	-3.2679	1.7382	33.0879	-6.8115	2.2465	-0.0092	-0.2595	0.7414	-0.5161	-0.1628	-0.9078	-0.6439	0.1292	0.1719	0.2707	-0.0686	-0.0508	0.0134	-0.0386	0.1447	-21.1842	45.0299	15.5482
15	1.4374	-0.6705	-1.4336	11.9162	-8.3664	8.4653	0.1954	-0.2655	0.257	-0.3612	-0.5479	-0.3431	-0.3053	-0.0819	0.3526	0.1221	-0.032	-0.0729	0.0996	-0.0589	0.0781	-19.571	35.5763	19.0489
16	18.9619	1.6576	0.585	20.0974	-7.954	3.2298	0.0169	-0.9138	0.2686	1.2081	0.0179	0.2337	0.1457	-0.0952	-0.0348	0.0936	-0.0858	-0.0755	0.1081	-0.0341	0.0546	-19.0707	29.1779	24.1559
17	14.9308	-0.8936	-0.5431	8.1804	-6.3754	5.0724	-0.1724	0.3589	-0.5802	-0.3394	-0.4533	-0.5047	0.5322	0.2551	0.6258	0.0992	-0.0049	-0.0351	0.0951	-0.048	0.0392	-14.6308	26.2682	22.0079
18	12.277	1.5924	-5.1768	11.5503	-10.401	22.8988	-0.0931	0.0092	-0.1459	-0.1206	-0.5383	-0.8879	0.3888	1.3237	0.6314	0.047	-0.0258	0.0024	0.1598	0.0762	0.0869	-12.559	33.1538	13.5884
19	7.0451	-6.9723	2.9	23.0273	-4.1155	11.2874	-0.2853	0.1134	0.7096	-0.4141	-0.348	-0.7957	-0.4397	0.7145	0.6333	0.0665	-0.1353	-0.03	0.0543	0.0428	0.0505	-17.8065	39.8411	6.6731
20	13.4228	-3.9494	-4.0045	1.166	1.3784	11.3079	-0.2635	-0.047	0.867	-0.844	-0.2615	1.03	-1.1482	-1.2436	0.525	0.4634	-0.0382	-0.1457	0.1683	0.1055	0.2968	-26.0394	43.2676	-3.7251
21	20.5591	4.7962	12.3333	14.9951	-4.9082	15.1852	-0.3242	0.067	0.3086	0.1556	0.1057	-0.0228	-0.6439	-0.031	0.2185	0.0662	0.009	-0.0028	0.0761	-0.0287	0.0541	-35.3808	36.5399	-6.3072
22	5.5361	-3.5665	1.3222	10.055	1.9178	1.3046	0.124	-0.0658	-0.0195	-0.1016	-0.2448	0.308	-0.206	-0.1291	0.1208	0.0637	-0.0249	-0.0108	0.0756	0.004	0.0271	-35.4389	29.742	-6.095
23	9.8436	-2.5638	-3.4499	9.918	4.4415	8.6586	-0.1846	-0.0004	0.1545	0.1694	0.0626	0.2968	0.4658	-0.0062	0.122	0.052	-0.0495	0.0194	0.0576	0.0263	-0.0282	-27.2923	23.4497	-7.6781
24	38.5545	-15.1998	-19.8843	14.8586	2.773	13.1501	-0.3238	2.5794	-2.071	-0.3662	0.0163	0.562	0.5112	-0.3556	0.3075	0.1443	-0.0234	-0.0041	0.118	-0.0461	0.1469	-22.431	19.9432	-12.7216
25	13.2404	6.2425	-3.5296	5.0077	-3.0784	1.9097	0.1705	-0.1023	-0.8124	-0.0394	-0.1278	-0.1784	0.4889	0.582	-0.0427	0.0936	0.0664	0.0604	0.1106	0.0197	0.1412	-14.2277	17.0262	-6.81
26	13.3673	-7.2668	-2.6741	10.8733	-0.0238	17.8857	0.199	-0.6617	-0.5721	-0.3334	-0.0791	-0.1022	1.0176	0.0122	-0.1199	0.0955	-0.0315	0.0157	0.0304	0.0863	0.046	-19.1373	17.1302	-2.3922
27	19.9203	-6.6732	-8.9215	15.4923	-3.1355	6.8248	-0.0119	-0.5479	-0.2653	0.023	0.0276	0.1102	-0.0936	0.0959	-0.0157	0.1352	-0.0006	-0.0106	0.1431	0.0078	0.0585	-27.3978	18.7447	0.3477
28	23.3607	-10.1587	7.0258	7.5221	2.7408	12.9342	-0.2606	0.1688	0.4583	0.7352	0.3663	-0.1531	0.6243	0.0784	-0.1058	0.1046	-0.0231	0.0136	0.069	0.0316	0.0629	-33.1966	23.5673	1.7925
29	15.1918	-4.6858	-2.9852	6.9947	5.7914	7.6724	-0.1458	0.0314	-0.2469	0.6201	-0.0826	0.0514	0.6634	0.1307	0.2285	0.0854	-0.0041	0.0535	0.0854	0.0468	0.0659	-41.4595	27.1764	5.3174
30	14.1558	2.5656	10.1148	2.0178	-1.4365	14.1126	-0.2456	-0.0922	0.5248	0.3613	0.362	0.3397	-0.8066	-0.1978	-0.1164	0.1232	0.0389	0.024	0.0524	-0.0129	0.1232	-36.1838	36.063	3.2168
31	17.2123	-4.4507	-3.8386	6.2647	4.5568	4.7689	-0.044	-0.1223	0.1379	0.2284	-0.1352	0.1066	-0.2146	0.2427	0.1792	0.0631	-0.0307	0.0223	0.0814	-0.0062	0.0209	-25.8286	31.0644	1.0222
32	19.8517	-1.2644	-0.2037	10.5299	-0.5655	0.0341	-0.1457	-0.6939	-0.4783	0.2873	-0.1974	-0.1802	0.3162	0.1342	0.3431	0.1292	0.0119	0.0208	0.1287	-0.0113	0.0385	-15.906	24.8658	0.4006
33	3.0164	4.0679	-0.1684	10.0275	1.8724	0.9799	-0.158	-0.5387	0.0005	0.5473	0.0052	-0.8535	0.2559	0.5522	0.1527	0.1534	0.0635	-0.0172	0.3367	0.0811	0.1583	-9.181	21.0007	-2.5218
34	20.1933	-4.7662	4.652	8.7571	2.6576	12.8799	-0.0315	0.3584	0.3391	-0.3978	-0.0863	-0.3742	-0.1268	0.7879	0.1178	0.0246	-0.0282	0.0818	0.0766	0.0603	0.0438	-11.7496	26.1672	-9.5952
35	14.115	0.1947	3.2665	5.1488	-0.3001	0.7791	-0.2838	0.0087	0.4279	-0.2545	-0.0259	-0.2511	0.2111	-0.1595	0.3097	0.1203	-0.0125	0.0372	0.1082	0.0196	0.0758	-21.4417	28.6779	-11.9425
36	18.0968	2.2433	6.2849	0.4992	2.0477	9.461	0.1272	-0.0227	-0.3867	-0.13	0.1358	-0.1566	-0.1024	-0.5319	-0.263	0.0747	-0.0435	-0.0007	0.0971	0.0111	0.0564	-29.7494	30.5937	-13.815
37	7.3963	0.5642	4.2642	0.1692	1.1612	7.9974	0.1791	-0.0979	0.6045	-0.0032	-0.0726	0.1663	-0.4503	-0.3662	-0.1065	0.0682	-0.0261	0.0059	0.0762	0.0338	0.0935	-25.9377	37.6423	-12.7725
38	10.8948	0.3549	8.4811	8.7601	-5.2846	10.1368	0.2273	-0.7022	-0.0109	0.1654	-0.1877	0.1278	-0.1172	-0.4437	-0.0395	0.0336	-0.058	0.0148	0.0853	-0.0134	0.058	-19.797	36.2375	-5.9688
39	9.8312	-3.731	7.3581	8.9928	-9.4528	11.3619	0.0765	-0.3033	0.042	0.1955	-0.3549	-0.1086	-0.1787	-0.0968	0.2784	0.0672	-0.0989	0.0367	0.1494	-0.0079	0.0555	-13.0369	33.9858	-1.4987
40	43.9332	-16.0622	9.0486	18.8904	8.0982	11.858	0.0184	-1.5705	1.2351	0.842	0.5033	-2.0137	-0.7462	1.5858	-0.5217	0.0516	-0.1638	-0.071	0.4491	0.0703	0.1688	-7.746	30.567	4.2413

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 10
2	X-RAY DIFFRACTION	2	A	11 - 17
3	X-RAY DIFFRACTION	3	A	18 - 22
4	X-RAY DIFFRACTION	4	A	23 - 28
5	X-RAY DIFFRACTION	5	A	29 - 36
6	X-RAY DIFFRACTION	6	A	37 - 45
7	X-RAY DIFFRACTION	7	A	46 - 51
8	X-RAY DIFFRACTION	8	A	52 - 57
9	X-RAY DIFFRACTION	9	A	58 - 63
10	X-RAY DIFFRACTION	10	A	64 - 69
11	X-RAY DIFFRACTION	11	A	70 - 75
12	X-RAY DIFFRACTION	12	A	76 - 81
13	X-RAY DIFFRACTION	13	A	82 - 89
14	X-RAY DIFFRACTION	14	A	90 - 96
15	X-RAY DIFFRACTION	15	A	97 - 102
16	X-RAY DIFFRACTION	16	A	103 - 107
17	X-RAY DIFFRACTION	17	A	108 - 113
18	X-RAY DIFFRACTION	18	A	114 - 119
19	X-RAY DIFFRACTION	19	A	120 - 128
20	X-RAY DIFFRACTION	20	A	129 - 135
21	X-RAY DIFFRACTION	21	B	6 - 10
22	X-RAY DIFFRACTION	22	B	11 - 19
23	X-RAY DIFFRACTION	23	B	20 - 24
24	X-RAY DIFFRACTION	24	B	25 - 30
25	X-RAY DIFFRACTION	25	B	31 - 36
26	X-RAY DIFFRACTION	26	B	37 - 41
27	X-RAY DIFFRACTION	27	B	42 - 47
28	X-RAY DIFFRACTION	28	B	48 - 52
29	X-RAY DIFFRACTION	29	B	53 - 60
30	X-RAY DIFFRACTION	30	B	61 - 66
31	X-RAY DIFFRACTION	31	B	67 - 76
32	X-RAY DIFFRACTION	32	B	77 - 82
33	X-RAY DIFFRACTION	33	B	83 - 90
34	X-RAY DIFFRACTION	34	B	91 - 96
35	X-RAY DIFFRACTION	35	B	97 - 103
36	X-RAY DIFFRACTION	36	B	104 - 108
37	X-RAY DIFFRACTION	37	B	109 - 115
38	X-RAY DIFFRACTION	38	B	116 - 120
39	X-RAY DIFFRACTION	39	B	121 - 126
40	X-RAY DIFFRACTION	40	B	127 - 132

-
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