PDB-3nke: High resolution structure of the C-terminal domain CRISP-associat...

ID or keywords:

Entry

Database: PDB / ID: 3nke

Title

High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from Escherichia coli str. K-12

Components

protein ygbT

Keywords

IMMUNE SYSTEM / CRISPR / Cas1 / YgbT / Nuclease / DNA recombination / DNA repair

Function / homology

Function and homology information

CRISPR-cas system / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / maintenance of CRISPR repeat elements / defense response to virus / Hydrolases; Acting on ester bonds / DNA repair / DNA damage response / protein homodimerization activity / DNA binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.4 Å

Authors

Nocek, B. / Skarina, T. / Beloglazova, N. / Savchenko, A. / Joachimiak, A. / Yakunin, A.

Citation

Journal: Mol.Microbiol. / Year: 2011
Title: A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.
Authors: Babu, M. / Beloglazova, N. / Flick, R. / Graham, C. / Skarina, T. / Nocek, B. / Gagarinova, A. / Pogoutse, O. / Brown, G. / Binkowski, A. / Phanse, S. / Joachimiak, A. / Koonin, E.V. / ...

History

Deposition	Jun 18, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 25, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Dec 17, 2014	Group: Data collection
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3nke.cif.gz	258.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3nke.ent.gz	211.9 KB	Display	PDB format
PDBx/mmJSON format	3nke.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3nke_validation.pdf.gz	481.8 KB	Display	wwPDB validaton report
Full document	3nke_full_validation.pdf.gz	488.5 KB	Display
Data in XML	3nke_validation.xml.gz	35.5 KB	Display
Data in CIF	3nke_validation.cif.gz	51.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nk/3nke ftp://data.pdbj.org/pub/pdb/validation_reports/nk/3nke	HTTPS FTP

-
Related structure data

Related structure data	3nkdC 3god C: citing same article (ref.)
Similar structure data	2xss-1 3wsz-d 6fkg-d 1cla-1 4m75-1 2jjs-d 9icu-d 8icg-d 4qde-2 3bla-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
Related items in Molecule of the Month	#181 - Jan 2015 Cascade and CRISPR similarity (9) #133 - Jan 2011 Nitric Oxide Synthase similarity (1)

Deposited unit

A: protein ygbT

B: protein ygbT

C: protein ygbT

hetero molecules

67.2 kDa, 3 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)	53.709, 90.047, 121.876
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	protein ygbT / CRISP-associated protein Cas1 Mass: 22118.281 Da / Num. of mol.: 3 / Fragment: UNP residues 92-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: ygbT, b2755, JW2725 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q46896
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO3 / SULFITE ION Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: O.O5 M MES 20% PEG 8k, 0.01 M Magnesium Chloride, 0.01M Adenelyl-imidodophosphate, 0.2M Ammonium sulfate, 0.3M NDSB211, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.4→45 Å / Num. all: 117000 / Num. obs: 115817 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / B_iso Wilson estimate: 22 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 28
Reflection shell	Resolution: 1.4→1.42 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5726

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Resolution: 1.4→33.2 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.952 / SU B: 1.997 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20067	5778	5 %	RANDOM
R_work	0.17656	-	-	-
obs	0.17777	109670	98.77 %	-

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: 14.603 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0.55 Å²	0 Å²
3-	-	-	-0.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→33.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4235	0	49	768	5052

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	4457
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3172
X-RAY DIFFRACTION	r_angle_refined_deg	1.591	1.993	6043
X-RAY DIFFRACTION	r_angle_other_deg	1.13	3	7681
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.401	5	576
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.008	21.872	187
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.253	15	771
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.173	15	53
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	685
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	4935
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	947
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.9	1.5	2791
X-RAY DIFFRACTION	r_mcbond_other	0.232	1.5	1124
X-RAY DIFFRACTION	r_mcangle_it	1.608	2	4492
X-RAY DIFFRACTION	r_scbond_it	2.559	3	1666
X-RAY DIFFRACTION	r_scangle_it	4.117	4.5	1537
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.4→1.436 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.262	419	-
R_work	0.248	8048	-
obs	-	-	99.06 %

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	0.8342	0.4116	0.0095	0.5236	0.7652	1.234	-0.0308	-0.0032	0.0233	0.0363	-0.0511	0.0294	-0.0076	-0.1803	0.082	0.0941	0.0242	-0.0043	0.1115	-0.0189	0.0987	3.9653	5.5106	31.4182
2	2.0096	0.0269	-1.0128	0.2266	0.1851	0.6089	-0.0569	0.1112	-0.0561	0.0343	-0.0104	0.0195	0.0529	-0.0469	0.0673	0.0966	-0.0157	0.0077	0.1045	-0.0194	0.0968	9.7977	-3.2315	18.1898
3	0.8796	0.5716	-0.1741	1.5722	-0.6757	0.4548	-0.014	0.0886	-0.0637	-0.1345	0.0046	0.0191	0.0759	0.0019	0.0094	0.1151	-0.0139	0.0035	0.0978	-0.0306	0.0772	12.1144	-8.5927	11.9092
4	2.8879	0.0227	-0.819	0.6191	0.379	0.2849	0.0836	-0.1036	-0.1494	0.0731	-0.0857	-0.0389	0.0391	0.0033	0.0021	0.1142	-0.0103	-0.0041	0.075	-0.0044	0.112	17.2676	-11.8283	19.2014
5	1.4309	0.512	0.3289	0.3419	-0.1861	0.512	0.0413	0.101	-0.0971	-0.0378	0.0319	0.0081	0.1018	0.0709	-0.0732	0.0932	0.0168	-0.006	0.0951	-0.0324	0.1024	34.0032	-8.0635	16.3383
6	3.0009	-6.031	-5.5757	19.4182	4.3171	4.7375	0.018	-0.4849	-0.5311	0.8675	-0.2728	-0.1187	0.0735	0.0888	0.2548	0.1641	-0.1113	-0.113	0.2515	0.1025	0.0974	34.7008	-9.4047	30.8828
7	1.4595	-1.6302	-0.087	2.1671	0.3132	0.2592	-0.0205	-0.112	0.0207	0.1135	0.042	-0.0558	0.028	-0.0034	-0.0214	0.0723	0.0151	-0.015	0.1224	-0.0237	0.1033	36.0623	-1.8542	27.8846
8	0.9663	0.3275	-0.45	0.7061	0.4031	0.95	-0.0403	-0.0787	0.0694	0.0325	0.0337	0.0246	0.0587	0.0656	0.0066	0.0758	0.0171	-0.0104	0.0958	-0.022	0.0956	16.9328	4.3875	30.332
9	0.8091	0.0467	-0.4025	-0.0007	0.1117	0.451	-0.0481	-0.0241	0.019	0.0179	0.0512	-0.0097	0.0607	0.0388	-0.0031	0.0896	0.0126	-0.0052	0.1071	-0.0156	0.102	24.9221	0.6572	24.7158
10	0.1694	-0.7598	-0.4565	1.8032	0.8403	1.6915	-0.0772	0.0717	0.0592	0.0668	0.0434	-0.0687	0.0258	0.0765	0.0339	0.041	-0.0074	-0.0145	0.1595	-0.0266	0.1171	45.039	2.8804	24.0471
11	2.2482	-1.0908	0.5565	0.6849	0.1401	0.6283	-0.0104	0.0727	-0.1844	0.0114	0.1119	0.0954	-0.1084	0.1396	-0.1015	0.0848	0.0017	0.0023	0.1037	-0.0123	0.1141	35.7127	11.7817	26.7084
12	2.926	1.1563	-0.0759	0.3808	0.0502	0.3839	-0.0401	0.1614	0.1723	-0.0045	0.0764	0.0552	-0.0509	-0.0368	-0.0363	0.0773	0.0078	-0.0148	0.0963	0.0072	0.1238	12.3329	10.3761	21.4116
13	2.234	-0.2675	-1.0509	0.1876	-0.6098	2.4739	-0.038	0.0187	0.0275	0.0652	-0.0082	-0.0036	-0.3007	-0.1254	0.0461	0.1422	0.0575	-0.0025	0.0794	0.0101	0.0873	9.0383	16.509	47.6926
14	0.5331	0.2391	0.1646	0.8832	-0.1779	0.2364	0.0736	0.0125	0.0127	0.0085	-0.0887	0.0115	-0.0262	-0.0932	0.0152	0.0925	0.0287	0.0087	0.1419	-0.0103	0.0722	5.0985	2.0641	59.44
15	2.8461	2.7384	4.2824	1.7979	3.2742	4.9025	0.0898	0.1179	-0.2007	0.1027	0.1146	0.0013	0.0318	0.1775	-0.2044	0.0758	0.0001	0.0242	0.1351	-0.0183	0.1432	0.0347	-6.2265	67.2719
16	-0.1505	0.5526	0.0681	1.5323	1.1409	2.1635	0.0037	-0.0061	0.0064	0.115	0.0182	-0.0238	0.2168	0.1131	-0.0219	0.1319	0.0271	-0.0137	0.0881	-0.0317	0.0829	7.6779	-12.493	59.8769
17	4.1548	1.0129	-0.2747	1.246	-0.4646	3.4402	-0.063	-0.1018	-0.0114	0.1073	-0.001	0.0423	0.5119	-0.0528	0.064	0.1948	-0.0115	0.0219	0.0041	-0.0231	0.0504	6.4083	-24.6953	47.5119
18	0.1764	-1.1945	0.0687	3.1128	0.1887	1.1503	-0.0371	-0.0116	0.0355	0.0648	0.0519	-0.0483	0.0927	-0.0119	-0.0147	0.1303	0.0164	-0.0005	0.0566	-0.0186	0.1019	11.7789	-15.0783	40.5863
19	0.3888	0.5408	0.0964	1.1529	0.0448	0.5945	0.0551	0.0386	-0.0427	0.0281	-0.0286	-0.0875	-0.0145	-0.0201	-0.0264	0.0885	0.0313	0.0045	0.1057	-0.003	0.0871	10.6278	1.0692	47.9057
20	0.7972	-0.8028	-0.0851	2.7548	0.544	0.0609	-0.0217	-0.0627	-0.0285	0.0317	0.0126	0.1097	0.153	-0.2022	0.009	0.1517	-0.0861	0.0104	0.141	-0.0119	0.09	2.15	-18.6269	41.2277
21	4.1469	-3.3601	-5.1781	5.6841	3.0437	3.0104	-0.1274	0.0739	-0.0748	-0.024	0.0493	0.0768	0.1754	-0.0327	0.0782	0.1353	0.0351	0.0102	0.0686	-0.0291	0.0878	9.9472	-20.5523	31.0473
22	3.2324	-3.4512	0.8405	4.0244	-1.3321	1.2162	-0.0746	0.0151	0.0915	0.0891	0.0313	-0.0616	0.1212	-0.1143	0.0433	0.0798	0.003	-0.0054	0.0842	-0.0098	0.1044	1.5045	-9.5283	33.4937
23	0.4457	0.1865	0.8936	1.7876	2.2504	3.5602	0.0215	-0.0238	0.0112	-0.0743	-0.0969	0.0535	-0.0375	-0.0998	0.0754	0.0784	0.0611	0.0039	0.1493	-0.0124	0.0673	-1.5398	3.2548	45.8324
24	12.6662	4.4206	-1.8911	8.9493	-5.0364	12.0307	0.3353	-0.0465	0.732	0.0649	-0.8071	0.2508	-0.4953	-0.6644	0.4717	0.0729	0.2125	0.0181	0.2182	-0.0514	0.0705	0.9832	13.9598	56.1769
25	1.1202	0.5333	0.8596	1.406	-0.0611	0.1713	-0.0124	-0.0415	0.004	-0.0463	0.0174	0.1619	-0.0864	0.0164	-0.005	0.1237	0.0231	-0.0207	0.0723	0.0011	0.1212	20.4364	19.7042	32.1361
26	0.2445	0.1022	0.306	0.3488	-0.3419	1.8131	-0.0103	0.0204	0.0089	0.0356	-0.0228	-0.0266	-0.0592	0.0419	0.0331	0.1128	-0.0127	-0.01	0.0857	-0.0004	0.0916	36.3915	20.436	42.0613
27	5.1023	-4.8163	-6.8968	4.4688	7.3769	16.7011	0.2704	-0.184	0.7546	0.0848	0.319	-0.8238	-0.1066	0.4657	-0.5894	0.1398	-0.0367	-0.0545	0.0492	-0.0348	0.2444	46.3018	22.2858	43.5913
28	2.2704	-0.6132	0.3624	0.1273	-0.0362	4.1884	-0.0569	0.0593	0.058	0.0043	-0.0135	-0.0054	0.2426	0.1517	0.0704	0.1022	0.0204	-0.0006	0.0998	0.014	0.0781	43.3242	12.8117	40.4964
29	1.0009	0.6996	-0.75	0.3213	-0.1201	0.7733	0.0254	-0.1074	-0.0429	-0.0258	-0.0516	-0.0136	0.0023	0.182	0.0262	0.0851	0.0541	0.0052	0.157	0.0316	0.0564	42.0425	5.6623	58.1761
30	6.6682	1.0809	-2.1866	3.9036	-0.4501	1.4685	0.0581	0.3649	-0.7108	0.0547	-0.0147	-0.0824	0.13	0.1108	-0.0434	0.08	0.0523	-0.0265	0.1109	-0.0266	0.1709	35.5044	-4.1891	56.3076
31	-0.0557	-0.1151	0.2175	0.5909	-0.5873	1.6552	0.0249	-0.0139	-0.0616	-0.0022	0.0619	0.0953	-0.0152	-0.0171	-0.0868	0.0826	0.0109	-0.0084	0.0896	0.0286	0.1158	24.1798	8.9946	46.0215
32	0.0385	-0.0527	0.6724	0.6527	0.0834	2.3151	0.0684	0.0104	-0.0703	-0.0052	0.0814	0.0589	0.079	0.1414	-0.1498	0.1077	0.0009	-0.0222	0.0848	-0.0083	0.1103	29.1962	9.3567	43.456
33	0.3729	-0.627	1.2871	1.3521	-1.4266	2.3464	0.0226	-0.0479	-0.0003	0.0334	0.0184	0.0487	-0.0279	0.0351	-0.041	0.0955	0.0053	-0.0019	0.1201	0.0412	0.0889	32.0348	5.7003	63.3934
34	0.8049	-0.5488	0.6108	2.7591	-0.7858	0.3784	0.0991	-0.0745	-0.0984	0.0397	-0.0636	0.0044	-0.0321	-0.0712	-0.0355	0.1134	0.0198	0.0167	0.0902	0.0411	0.1089	21.262	5.1486	62.5221
35	0.9356	0.4495	-2.1128	1.4193	-1.1778	3.3813	-0.0141	0.0126	-0.0354	0.129	0.0443	0.0636	-0.1191	0.0461	-0.0302	0.1456	0.0193	0.0164	0.0568	0.0107	0.1031	23.5891	21.7475	47.1618
36	17.1251	-1.1727	4.6222	6.2995	1.802	1.1996	0.161	0.0977	0.1945	0.1205	-0.3423	0.4783	-0.3355	0.1634	0.1813	0.3302	-0.0119	0.0157	0.0031	-0.0152	0.0905	23.9427	28.1377	35.0841

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	94 - 108
2	X-RAY DIFFRACTION	2	A	109 - 123
3	X-RAY DIFFRACTION	3	A	124 - 134
4	X-RAY DIFFRACTION	4	A	135 - 143
5	X-RAY DIFFRACTION	5	A	144 - 163
6	X-RAY DIFFRACTION	6	A	164 - 172
7	X-RAY DIFFRACTION	7	A	173 - 186
8	X-RAY DIFFRACTION	8	A	187 - 208
9	X-RAY DIFFRACTION	9	A	209 - 234
10	X-RAY DIFFRACTION	10	A	235 - 244
11	X-RAY DIFFRACTION	11	A	245 - 257
12	X-RAY DIFFRACTION	12	A	258 - 280
13	X-RAY DIFFRACTION	13	B	92 - 101
14	X-RAY DIFFRACTION	14	B	102 - 124
15	X-RAY DIFFRACTION	15	B	125 - 131
16	X-RAY DIFFRACTION	16	B	132 - 151
17	X-RAY DIFFRACTION	17	B	152 - 164
18	X-RAY DIFFRACTION	18	B	172 - 190
19	X-RAY DIFFRACTION	19	B	191 - 223
20	X-RAY DIFFRACTION	20	B	224 - 238
21	X-RAY DIFFRACTION	21	B	239 - 246
22	X-RAY DIFFRACTION	22	B	247 - 258
23	X-RAY DIFFRACTION	23	B	259 - 274
24	X-RAY DIFFRACTION	24	B	275 - 281
25	X-RAY DIFFRACTION	25	C	92 - 107
26	X-RAY DIFFRACTION	26	C	108 - 125
27	X-RAY DIFFRACTION	27	C	126 - 132
28	X-RAY DIFFRACTION	28	C	133 - 140
29	X-RAY DIFFRACTION	29	C	141 - 162
30	X-RAY DIFFRACTION	30	C	163 - 178
31	X-RAY DIFFRACTION	31	C	179 - 207
32	X-RAY DIFFRACTION	32	C	208 - 223
33	X-RAY DIFFRACTION	33	C	224 - 238
34	X-RAY DIFFRACTION	34	C	239 - 261
35	X-RAY DIFFRACTION	35	C	262 - 274
36	X-RAY DIFFRACTION	36	C	275 - 281

-
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