PDB-3dns: The N-terminal domain of Ribosomal-protein-alanine acetyltransfer...

ID or keywords:

Entry

Database: PDB / ID: 3dns

Title

The N-terminal domain of Ribosomal-protein-alanine acetyltransferase from Clostridium acetobutylicum ATCC 824

Components

Ribosomal-protein-alanine acetyltransferase

Keywords

TRANSFERASE / N-terminal domain of Ribosomal-protein-alanine acetyltransferase / MCSG / PSI / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / Ribosomal protein

Function / homology

Function and homology information

[ribosomal protein uS5]-alanine N-acetyltransferase / protein-N-terminal-alanine acetyltransferase activity / cytoplasm
Similarity search - Function

Biological species

Clostridium acetobutylicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Nocek, B. / Hendricks, R. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The N-terminal domain of Ribosomal-protein-alanine acetyltransferase from Clostridium acetobutylicum ATCC 824
Authors: Nocek, B. / Hendricks, R. / Cobb, G. / Joachimiak, A.

History

Deposition	Jul 2, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	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_ref_seq_dif 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_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3dns.cif.gz	73.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3dns.ent.gz	57.9 KB	Display	PDB format
PDBx/mmJSON format	3dns.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dn/3dns ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dns	HTTPS FTP

-
Related structure data

Similar structure data	6bgc-2 2odl-d 2w5k-d 2v7m-d 4jzs-d 3zev-1 3up6-2 4etz-1 5nf4-2 5e6c-d 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: apc60332.2

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: Ribosomal-protein-alanine acetyltransferase

B: Ribosomal-protein-alanine acetyltransferase

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

1

A: Ribosomal-protein-alanine acetyltransferase

B: Ribosomal-protein-alanine acetyltransferase

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

2

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	59.619, 59.619, 196.448
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Details

authors state that the biological unit is Unknown.

#1: Protein	Ribosomal-protein-alanine acetyltransferase / Acetylating enzyme for N-terminal of ribosomal protein S5 Mass: 16123.908 Da / Num. of mol.: 2 / Fragment: residues 1-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CA_C0152 / Plasmid: pmcsg7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97MP0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.56 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M NaCl, 0.1 M citrate ph 5.5 40% propanediol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
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: Jun 18, 2008 / 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: 2.1→30 Å / Num. all: 39476 / Num. obs: 38325 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / R_merge(I) obs: 0.075 / Net I/σ(I): 21.1
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.32 / Mean I/σ(I) obs: 4.2 / % possible all: 99

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.1→30 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.912 / SU B: 9.296 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.202 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24607	1078	5.1 %	RANDOM
R_work	0.19726	-	-	-
all	0.19967	20939	-	-
obs	0.19967	19861	97.01 %	-

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: 22.555 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.28 Å²	0 Å²	0 Å²
2-	-	1.28 Å²	0 Å²
3-	-	-	-2.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2153	0	0	193	2346

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	2189
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1544
X-RAY DIFFRACTION	r_angle_refined_deg	1.772	1.964	2927
X-RAY DIFFRACTION	r_angle_other_deg	0.942	3	3774
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.566	5	258
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.594	25.094	106
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.311	15	445
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.828	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	322
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2362
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	454
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	374
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	1579
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	1049
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	1221
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	135
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	0.248	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.213	0.2	40
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.31	0.2	14
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	1.074	1.5	1603
X-RAY DIFFRACTION	r_mcbond_other	0.248	1.5	532
X-RAY DIFFRACTION	r_mcangle_it	1.316	2	2091
X-RAY DIFFRACTION	r_scbond_it	2.031	3	1045
X-RAY DIFFRACTION	r_scangle_it	2.758	4.5	836
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.102→2.156 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.259	81	-
R_work	0.17	1463	-
obs	-	-	98.85 %

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	3.7216	-7.4223	0.8309	19.0676	-6.353	5.3558	0.426	-0.3031	0.4151	1.3359	-0.2189	-0.539	0.472	-0.2941	-0.2071	0.1643	-0.1024	-0.067	0.253	-0.0114	-0.0021	27.0277	12.6979	72.0885
2	11.992	18.7173	3.758	45.3742	6.3452	1.1919	0.4124	-0.7525	0.5693	1.773	-0.4385	0.5887	0.2854	-0.1285	0.0261	0.1848	-0.0526	0.0453	0.2026	-0.0366	0.0474	23.931	15.9631	69.6355
3	13.8106	-6.0993	-7.3279	19.8583	14.5225	11.3092	-0.0786	0.1661	-1.4496	0.9088	-0.7052	0.3844	1.6237	-1.2522	0.7838	0.2147	-0.0833	0.1134	0.1765	-0.0105	0.1844	18.4115	2.2593	62.1709
4	3.1028	-1.4741	-4.8814	7.274	4.6409	8.4996	-0.4327	-0.33	0.0512	0.274	0.116	-0.0291	0.3277	-0.0657	0.3167	0.1082	-0.0093	0.0203	0.1841	0.0227	0.0705	20.6034	10.6598	63.2746
5	8.971	5.6387	3.8917	15.1993	11.2905	12.0924	0.2031	-0.5524	0.1022	0.302	0.0048	-0.144	-0.4953	-0.1558	-0.2078	0.2044	0.0287	-0.0236	0.1851	-0.0197	0.0524	17.7633	20.8226	69.5586
6	4.4585	-4.3144	-1.1734	6.3541	2.6693	3.785	-0.1113	-0.0749	-0.1284	-0.0745	0.1549	0.0982	-0.0485	-0.0114	-0.0436	0.104	-0.0658	0.0687	0.1392	0.0023	0.0916	23.8737	7.9626	57.1127
7	5.4392	-3.6478	-0.7195	3.0483	-0.0547	1.0536	0.026	-0.1102	-0.163	0.0106	-0.0175	0.1325	0.185	-0.0883	-0.0085	0.1776	-0.034	0.0383	0.1384	0.0269	0.0897	33.4238	1.178	55.5106
8	8.5972	-7.1043	-0.7067	15.8138	6.7075	3.8293	-0.2743	0.2089	0.3381	-0.0967	-0.2049	-0.0777	-0.0884	0.0867	0.4792	0.1326	-0.0502	0.0263	0.1626	0.0539	0.041	20.6625	21.8292	56.4854
9	13.7221	-8.0651	2.2761	19.8891	-7.4581	16.4443	-0.1177	-0.3913	0.5636	0.5089	-0.1881	0.1151	-0.3597	-0.3193	0.3058	0.0645	-0.03	-0.0206	0.0714	-0.0314	0.1597	27.8751	24.7545	62.3853
10	5.0452	-2.7886	-0.831	12.7429	-3.6846	7.727	0.0899	-0.2906	0.5017	0.0221	-0.1311	-0.2282	0.2514	0.0527	0.0412	0.1152	-0.0677	0.0242	0.1692	-0.0077	0.1171	31.6358	17.3188	64.5704
11	0.8977	-0.6527	-2.3051	2.8416	0.8849	6.1834	-0.0103	-0.1535	-0.1156	0.295	-0.2294	-0.0833	0.1784	0.2669	0.2397	0.1712	-0.0479	-0.0004	0.1684	0.0421	0.0635	35.7734	5.5474	64.5382
12	0.2619	-1.4188	0.472	9.2796	-2.9968	0.9721	-0.2853	0.3437	0.3804	0.3787	-0.1948	-0.3763	0.0558	0.0406	0.48	0.1364	-0.019	0.0341	0.1638	0.0373	0.1135	33.9795	8.7492	53.7175
13	9.4868	-3.0664	5.6663	19.2399	7.9958	18.3181	-0.2057	-0.1324	0.2469	-0.6124	-0.0601	0.3756	-0.8709	0.2387	0.2658	0.124	-0.0414	0.0504	0.1187	0.0486	0.085	26.6631	20.5362	49.8944
14	15.7732	5.5022	-3.7969	10.4403	-8.7175	21.7959	0.6138	-0.8962	1.032	-0.4496	-0.1111	0.4285	-0.3975	0.1669	-0.5027	0.0686	-0.0764	0.0278	0.0922	-0.037	0.1071	36.4063	20.7116	56.5456
15	9.6822	0.5943	2.7442	2.8617	0.5736	0.8359	0.0826	0.3395	0.2621	-0.3042	-0.1007	-0.0411	-0.2701	0.0528	0.0181	0.1433	0.0243	0.0751	0.204	0.0305	0.0295	29.6002	14.2817	43.6998
16	54.4357	9.9732	-13.385	20.7856	9.7633	23.4264	-0.6606	0.8085	3.518	-0.4016	-0.0933	1.3547	-1.8077	-0.6948	0.7538	0.1915	0.1365	-0.1042	0.2114	0.0499	0.2836	16.0178	19.3988	41.118
17	14.0604	-4.18	9.7176	3.9469	-3.2372	6.761	0.0757	0.2941	0.2394	-0.0182	-0.1834	-0.1403	-0.3762	0.0999	0.1077	0.1182	0.0114	0.0905	0.1459	0.0475	0.0492	32.4182	14.4137	49.2213
18	17.0172	5.7944	1.3758	24.311	6.0938	15.8656	0.1995	0.2761	0.3403	0.2583	0.0989	-1.5733	0.6953	1.077	-0.2984	0.0191	0.0034	-0.0701	0.2185	0.0272	0.0942	44.3656	9.8374	62.4494
19	20.3147	-21.4872	-13.2423	23.0393	16.0977	22.6512	0.0878	1.9071	0.5551	-0.5146	-1.043	0.298	-0.2022	-2.5702	0.9552	0.0826	0.0071	-0.1223	0.3198	-0.1019	0.1755	26.8041	-11.7163	25.6697
20	10.9721	0.7539	-1.5612	9.4934	0.7075	7.2792	0.4006	-0.3504	-0.3027	0.9835	0.1416	0.8787	0.8867	-1.0391	-0.5422	0.1523	0.003	-0.0416	0.1402	-0.131	0.2687	22.6978	-13.1536	40.0538
21	4.8367	-1.0959	-5.9977	5.8653	2.2469	16.6675	-0.0406	0.226	-0.3304	0.3841	-0.2669	0.6723	0.4278	-0.063	0.3075	0.0373	-0.077	0.0736	0.0938	-0.0889	0.1455	25.8489	-10.3833	40.6235
22	5.444	-0.7147	-2.3964	10.8121	1.5783	4.1957	0.1736	0.5632	-0.4524	-0.557	0.2885	0.339	0.4305	0.451	-0.4621	0.1166	-0.0062	-0.0148	0.1611	-0.0825	0.1815	32.3639	-18.8547	31.0261
23	1.0361	0.5127	-0.9466	0.2608	-0.3792	1.9925	-0.1815	0.1281	-0.1355	0.4557	0.0997	0.1238	0.173	0.1126	0.0818	0.1477	0.0048	0.0281	0.1327	-0.0182	0.1121	27.5956	-5.3228	43.0686
24	5.8439	-5.2788	-0.0724	5.9359	-0.3025	0.5447	0.1159	0.1768	-0.3374	-0.0253	-0.201	0.3544	-0.1565	-0.103	0.0851	0.1021	0.0065	0.0229	0.2035	-0.0355	0.087	22.5448	4.0556	42.2832
25	12.9167	-9.7408	-3.5503	8.4056	0.4569	5.628	0.2472	-0.9339	0.1371	0.3126	-0.2694	-0.0874	-0.053	0.2162	0.0222	0.1982	-0.031	-0.0103	0.1345	-0.0225	0.0827	39.47	-10.5393	39.4801
26	7.7541	-7.8265	4.7236	9.3226	-8.5145	12.7424	0.3585	0.4153	0.0874	-0.5114	-0.582	-0.5505	0.1561	-0.201	0.2235	0.222	0.0443	0.0456	0.1354	0.0559	0.0626	41.5545	-9.1026	28.8296
27	3.4043	-2.8569	-1.082	9.5421	5.5962	3.4202	0.9777	0.5	-0.1235	-0.7871	-0.8421	0.2165	0.436	0.1663	-0.1355	0.1664	0.0786	0.0266	0.2118	-0.0224	0.0538	33.3527	-6.9809	28.4463
28	1.4	-2.2407	2.3873	3.7596	-3.6996	4.1554	0.3271	0.3916	0.1049	-0.4246	-0.2793	0.4156	-0.1195	-0.342	-0.0478	0.1128	0.0555	-0.0004	0.2886	-0.0719	0.0553	26.3731	-2.7564	31.6597
29	6.0142	-4.1842	-7.0634	11.6075	-3.4236	16.2896	0.2771	0.3522	-0.2884	-1.2619	-0.7311	0.7864	-0.0212	-0.5878	0.454	0.0788	0.0226	-0.0283	0.3147	-0.134	0.0314	19.755	-0.0988	31.7634
30	1.4356	0.0151	-0.7541	1.0665	0.4576	1.3458	0.0486	0.3052	-0.0064	-0.0503	-0.2582	0.1366	0.0891	-0.0466	0.2095	0.1127	0.0197	0.0227	0.2115	-0.0534	0.0911	23.0021	4.1609	37.4506
31	1.971	0.5937	1.3276	0.182	0.113	26.4791	0.2441	-0.0569	0.0605	-0.1162	-0.2386	-0.2885	0.3081	0.7349	-0.0055	0.1541	0.0474	0.0408	0.1523	0.0603	0.113	41.2429	-1.1895	36.9966
32	2.4745	-3.0147	-4.277	13.55	6.1096	7.4742	0.4932	-0.0443	0.1676	0.1017	-0.0251	0.0395	-0.22	0.4688	-0.468	0.1733	0.0831	0.0142	0.2654	0.0339	0.0067	35.5754	4.9703	31.3121
33	0.5926	-1.4194	2.5073	9.0262	-5.144	10.7395	-0.1133	-0.1027	0.0648	0.1225	-0.3083	-0.7365	-0.3734	0.3044	0.4216	0.049	0.0058	0.0394	0.1994	0.0831	0.134	39.8721	4.3375	47.7061
34	13.9387	-6.4801	0.3601	46.6479	-11.1907	18.0654	0.3214	-0.1136	-0.7734	0.4793	-0.5671	-0.0705	1.103	1.4798	0.2457	0.1211	0.1298	0.0302	0.1896	0.0585	0.1373	45.9408	-4.6273	51.4374
35	8.9281	-4.243	8.7073	3.0273	-4.1378	9.3666	0.0818	0.3929	0.0734	0.0267	-0.1925	-0.2561	-0.3701	0.2318	0.1107	0.1169	0.013	0.083	0.1484	0.0061	0.0697	34.864	5.2952	39.2207
36	8.6758	7.1886	-2.9703	7.3749	2.1404	15.9437	0.4316	1.6867	1.0193	-1.5506	-0.3147	0.2378	-0.3252	-0.7749	-0.117	0.188	0.1517	-0.061	0.2457	-0.0233	0	23.1286	8.6285	27.8129

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	0 - 5	3 - 8
2	X-RAY DIFFRACTION	2	A	A	6 - 10	9 - 13
3	X-RAY DIFFRACTION	3	A	A	11 - 17	14 - 20
4	X-RAY DIFFRACTION	4	A	A	18 - 22	21 - 25
5	X-RAY DIFFRACTION	5	A	A	23 - 28	26 - 31
6	X-RAY DIFFRACTION	6	A	A	29 - 37	32 - 40
7	X-RAY DIFFRACTION	7	A	A	38 - 47	41 - 50
8	X-RAY DIFFRACTION	8	A	A	48 - 55	51 - 58
9	X-RAY DIFFRACTION	9	A	A	56 - 61	59 - 64
10	X-RAY DIFFRACTION	10	A	A	62 - 67	65 - 70
11	X-RAY DIFFRACTION	11	A	A	68 - 79	71 - 82
12	X-RAY DIFFRACTION	12	A	A	80 - 84	83 - 87
13	X-RAY DIFFRACTION	13	A	A	85 - 90	88 - 93
14	X-RAY DIFFRACTION	14	A	A	91 - 99	94 - 102
15	X-RAY DIFFRACTION	15	A	A	100 - 110	103 - 113
16	X-RAY DIFFRACTION	16	A	A	111 - 115	114 - 118
17	X-RAY DIFFRACTION	17	A	A	116 - 124	119 - 127
18	X-RAY DIFFRACTION	18	A	A	125 - 129	128 - 132
19	X-RAY DIFFRACTION	19	B	B	2 - 6	5 - 9
20	X-RAY DIFFRACTION	20	B	B	7 - 16	10 - 19
21	X-RAY DIFFRACTION	21	B	B	17 - 22	20 - 25
22	X-RAY DIFFRACTION	22	B	B	23 - 28	26 - 31
23	X-RAY DIFFRACTION	23	B	B	29 - 37	32 - 40
24	X-RAY DIFFRACTION	24	B	B	38 - 48	41 - 51
25	X-RAY DIFFRACTION	25	B	B	49 - 53	52 - 56
26	X-RAY DIFFRACTION	26	B	B	54 - 59	57 - 62
27	X-RAY DIFFRACTION	27	B	B	60 - 64	63 - 67
28	X-RAY DIFFRACTION	28	B	B	65 - 69	68 - 72
29	X-RAY DIFFRACTION	29	B	B	70 - 74	73 - 77
30	X-RAY DIFFRACTION	30	B	B	75 - 84	78 - 87
31	X-RAY DIFFRACTION	31	B	B	85 - 93	88 - 96
32	X-RAY DIFFRACTION	32	B	B	94 - 101	97 - 104
33	X-RAY DIFFRACTION	33	B	B	102 - 110	105 - 113
34	X-RAY DIFFRACTION	34	B	B	111 - 116	114 - 119
35	X-RAY DIFFRACTION	35	B	B	117 - 124	120 - 127
36	X-RAY DIFFRACTION	36	B	B	125 - 129	128 - 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://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