PDB-3pe9: Structures of Clostridium thermocellum CbhA fibronectin(III)-like...

ID or keywords:

Entry

Database: PDB / ID: 3pe9

Title

Structures of Clostridium thermocellum CbhA fibronectin(III)-like modules

Components

Fibronectin(III)-like module

Keywords

UNKNOWN FUNCTION / CbhA /

beta-sandwich /

Cellulosome

Function / homology

Function and homology information

Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds /

cellulose binding /

cellulase activity / cellulose catabolic process /

metal ion binding
Similarity search - Function

Biological species

Clostridium thermocellum (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 1.69 Å

Authors

Alahuhta, P.M. / Lunin, V.V.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex.
Authors: Brunecky, R. / Alahuhta, M. / Bomble, Y.J. / Xu, Q. / Baker, J.O. / Ding, S.Y. / Himmel, M.E. / Lunin, V.V.

History

Deposition	Oct 25, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2012	Group: Database references
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3pe9.cif.gz	171 KB	Display	PDBx/mmCIF format
PDB format	pdb3pe9.ent.gz	139 KB	Display	PDB format
PDBx/mmJSON format	3pe9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/3pe9 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/3pe9	HTTPS FTP

-
Related structure data

Related structure data	3pddC 3pdgC C: citing same article (ref.)
Similar structure data	3pdg-d 2jzk-d 6dyk-3 6dyk-4 1nct-d 6dye-1 4h6h-1 2rdk-2 2l2n-d 1n02-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

3pddC

3pdgC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (2) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Fibronectin(III)-like module

B: Fibronectin(III)-like module

C: Fibronectin(III)-like module

D: Fibronectin(III)-like module

hetero molecules

45.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fibronectin(III)-like module

hetero molecules

defined by author&software
11.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fibronectin(III)-like module

hetero molecules

defined by author&software
11.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Fibronectin(III)-like module

hetero molecules

defined by author&software
11.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Fibronectin(III)-like module

hetero molecules

defined by author&software
11.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	42.128, 103.281, 45.632
Angle α, β, γ (deg.)	90.00, 106.53, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

This structure contains the second fibronectin(III)-like module from clostridium thermocellum CbhA. The biological assembly cannot be determine without the whole enzyme.

#1: Protein	Fibronectin(III)-like module / Glycoside hydrolase / family 9 Mass: 10938.033 Da / Num. of mol.: 4 / Fragment: unp residues 915-1003 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cthe_0413 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DCH2
#2: Chemical	ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.18 Å³/Da / Density % sol: 43.45 %
Crystal grow	Method: vapor diffusion / pH: 6.2 Details: 0.2 M Ammonium iodide and 20% (w/v) Polyethylene glycol 3,350, pH 6.2, VAPOR DIFFUSION, temperature 100K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
Detector	Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 9, 2009 / Details: Helios mirrors
Radiation	Monochromator: Helios mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.69→25 Å / Num. all: 41325 / Num. obs: 41325 / % possible obs: 98.8 % / Redundancy: 5.67 %
Reflection shell	Resolution: 1.69→1.78 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 2.53 / R_sym value: 0.4056 / % possible all: 97.6

-
Processing

Software

Name	Version	Classification
PROTEUM PLUS		data collection
SHELX		model building
REFMAC	5.5.0109	refinement
SAINT		data reduction
PROTEUM PLUS		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.69→25 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.944 / SU B: 5.441 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22861	1843	5 %	RANDOM
R_work	0.18188	-	-	-
obs	0.18442	34722	87.53 %	-
all	-	34722	-	-

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: 16.602 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4 Å²	0 Å²	-0.15 Å²
2-	-	-0.43 Å²	0 Å²
3-	-	-	0.74 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2718	0	11	592	3321

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	3012
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1974
X-RAY DIFFRACTION	r_angle_refined_deg	1.902	1.957	4121
X-RAY DIFFRACTION	r_angle_other_deg	1.001	3	4866
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.002	5	395
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.142	25.664	143
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.14	15	512
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.906	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	458
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3512
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	585
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	1.103	1.5	1906
X-RAY DIFFRACTION	r_mcbond_other	0.392	1.5	757
X-RAY DIFFRACTION	r_mcangle_it	1.731	2	3112
X-RAY DIFFRACTION	r_scbond_it	2.746	3	1106
X-RAY DIFFRACTION	r_scangle_it	4.031	4.5	1009
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.69→1.734 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	122	-
R_work	0.282	2236	-
obs	-	-	77.34 %

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	2.8058	1.2423	1.4853	2.4735	1.0951	3.1741	-0.1267	0.2083	-0.005	-0.2556	0.0962	0.0566	-0.1704	0.0752	0.0305	0.0471	0.016	0.014	0.0508	0.0151	0.0656	18.62	56.289	30.9319
2	2.8361	-0.1882	1.2606	2.0789	0.5113	5.9328	-0.0281	0.1154	-0.0966	-0.1332	0.002	0.0954	-0.0305	-0.1283	0.0262	0.0258	0.0116	0.0297	0.0269	0.0284	0.0834	12.9614	53.2626	34.7611
3	2.0452	-0.0922	-0.6243	2.1176	-0.2123	1.6099	0.081	0.1914	-0.2378	-0.2334	0.0111	0.2435	0.1854	-0.2115	-0.0921	0.1035	0.0024	-0.0058	0.0437	0.01	0.1107	10.7013	42.9817	31.2868
4	4.2837	1.1013	-0.0404	9.2098	-1.9477	3.3792	-0.0282	-0.1568	-0.2064	0.1633	0.1506	0.7532	0.2735	-0.547	-0.1224	0.103	-0.0039	-0.0032	0.1263	-0.0007	0.0932	3.0543	48.0649	30.6226
5	2.9385	0.2525	-0.0392	1.5142	0.2965	1.7062	-0.0049	-0.0515	0.0137	0.0108	-0.0063	-0.0212	-0.0004	0.0075	0.0112	0.0479	-0.001	0.0051	0.0148	0.0043	0.0268	18.073	52.1587	40.8264
6	7.1435	4.8963	2.9775	7.0923	2.5676	4.3903	-0.0034	0.2349	-0.325	-0.2021	0.035	0.1967	0.2784	-0.2586	-0.0316	0.1035	0.0273	0.0206	0.0974	0.0041	0.0864	12.6108	41.6017	28.2704
7	1.1705	0.6214	0.7959	2.5703	1.4751	2.7179	0.0496	0.1197	-0.249	-0.0686	0.0243	0.0727	0.2044	-0.1491	-0.0739	0.0749	0.0242	0.0088	0.0899	0.0032	0.0923	19.55	46.3272	29.0075
8	2.8564	-1.5873	1.8074	4.4156	0.9064	5.1633	-0.0479	-0.2931	0.4643	0.2879	0.0459	-0.0329	-0.4212	-0.1222	0.002	0.1201	-0.0426	0.0715	0.0935	-0.0353	0.1724	25.5319	60.2979	46.1162
9	0.7383	1.5235	0.2725	4.5505	3.4679	7.396	-0.0433	0.1114	0.0959	-0.1772	-0.0014	0.302	-0.022	-0.2652	0.0446	0.096	0.0114	-0.0026	0.1138	-0.0057	0.1162	11.2764	23.2161	23.7561
10	2.231	0.7588	-0.2245	2.0814	0.2988	0.6329	-0.0382	0.0817	0.0261	-0.0894	0.0074	0.0123	-0.1246	0.0765	0.0308	0.0493	0.0033	-0.0008	0.043	0.0044	0.0645	19.0704	32.9404	37.9541
11	0.2414	0.2248	1.1268	1.3367	1.933	9.3129	-0.0465	0.071	0.0451	-0.1783	-0.0141	0.0977	-0.2514	-0.139	0.0606	0.0386	-0.0135	-0.0022	0.0804	0.0211	0.0588	11.6466	28.9894	37.4718
12	0.3827	0.0113	-0.0285	0.1983	-0.1578	0.152	-0.013	0.3061	-0.3221	-0.2893	0.0801	0.0495	0.2176	-0.1306	-0.0671	0.4286	-0.0806	-0.0431	0.3935	-0.1232	0.3926	4.1539	18.1793	19.9671
13	5.6881	0.3515	1.3235	3.3994	-0.097	2.9169	0.0717	0.1531	-0.1517	-0.242	-0.01	0.2691	0.1432	-0.233	-0.0617	0.0913	0.0057	0.0288	0.0529	0.0013	0.0679	10.4727	16.9465	33.6437
14	9.4978	-0.4293	4.6012	4.8306	-0.6766	6.3452	0.1712	0.1451	-0.2694	-0.515	-0.0243	0.5971	0.2783	-0.6146	-0.1469	0.1416	-0.0049	-0.0023	0.121	-0.0012	0.1285	4.2825	19.2037	35.3427
15	1.1842	-0.1883	-0.0043	1.4532	0.5818	2.1229	0.028	0.1368	-0.1135	-0.1136	-0.0305	0.1636	0.1194	-0.1694	0.0025	0.0472	0.0074	0.0065	0.0438	0.01	0.0543	13.8034	20.9937	34.1716
16	3.8327	0.2485	0.7631	2.1998	-0.0722	4.6739	0.0124	-0.1717	0.1252	0.2192	0.1001	-0.1396	0.0318	0.1498	-0.1124	0.044	0.0036	-0.0077	0.0506	0.0134	0.0716	24.576	31.8258	42.6315
17	2.2063	0.1069	-2.0146	8.0064	-1.3852	2.2584	-0.0943	-0.2588	-0.0964	0.3756	0.0622	-0.169	0.0188	0.0797	0.0321	0.05	-0.0007	0.0059	0.1421	0.0253	0.0846	5.0458	24.846	60.8348
18	3.0244	-0.9903	-0.9047	3.4064	-0.7102	2.8721	-0.0009	-0.0139	0.079	0.0408	-0.015	0.0086	-0.292	-0.1217	0.0159	0.049	-0.0077	-0.0052	0.0471	-0.0018	0.0801	-3.3788	33.3645	47.4705
19	2.1135	0.0496	0.5789	1.403	-0.0727	3.8937	0.0216	-0.2952	-0.272	0.2557	-0.023	-0.2374	0.275	0.25	0.0014	0.1021	-0.0175	0.0071	0.1107	-0.0055	0.1404	10.0967	23.1714	57.5905
20	4.9813	-0.132	-0.177	2.707	-0.0362	1.7633	0.0709	0.0491	-0.2124	0.0376	-0.004	-0.0899	0.1337	0.0956	-0.0669	0.0505	0.0009	0.0087	0.0174	-0.0054	0.0272	6.8119	17.6001	51.1911
21	7.669	3.2389	2.1683	5.8358	-1.6061	11.4701	0.035	0.0657	0.079	0.0099	-0.1149	-0.4738	0.0792	0.45	0.0799	0.0522	-0.0053	0.0075	0.0469	-0.0024	0.0684	14.5709	24.9617	54.4773
22	1.5496	-0.1776	0.4953	0.9961	-0.5145	1.4548	0.017	0.0051	0.0005	-0.0334	0.0089	0.046	0.0211	-0.0295	-0.0259	0.0289	-0.0026	0.0054	0.0128	-0.0146	0.0219	0.7055	22.5616	49.178
23	6.8874	-4.0214	-0.4187	5.663	0.1119	2.1669	-0.0339	-0.0202	-0.1805	0.0564	-0.0002	-0.1772	0.2158	0.2341	0.0342	0.0845	-0.0259	-0.0001	0.0738	-0.0025	0.0508	6.423	13.7018	60.4933
24	3.4162	-1.0623	1.9573	2.2622	-0.7155	6.3593	0.0301	0.1248	0.1421	-0.1275	0.0579	0.0758	-0.1153	-0.093	-0.088	0.0318	0.0004	0.0032	0.0401	-0.0194	0.0691	-7.6381	31.2546	45.2625
25	0.1134	-0.3058	0.225	5.4259	-4.5473	4.0697	-0.0188	-0.1021	-0.0163	0.2013	-0.0836	-0.2728	-0.0523	0.1986	0.1024	0.0941	0.0372	-0.0452	0.1598	-0.0193	0.1134	7.4891	49.8316	61.3011
26	2.5167	-1.0485	-0.2977	2.3514	-0.446	0.8204	-0.0395	-0.0575	0.0209	0.0648	0.0072	-0.0456	-0.0305	0.005	0.0322	0.0313	-0.0177	0.0019	0.0217	-0.0065	0.0477	1.9031	57.0913	48.085
27	6.8332	-1.4867	1.3622	3.8696	-0.6129	2.6782	0.0907	-0.0145	-0.102	0.1375	-0.0343	-0.195	0.1281	0.1921	-0.0563	0.082	-0.0058	0.0331	0.0421	-0.0003	0.0543	8.5301	43.0326	52.6698
28	1.4185	-0.2367	0.5424	2.4562	-0.381	2.224	0.0209	0.0354	-0.0405	0.0975	-0.0212	-0.1906	0.0638	0.2343	0.0002	0.043	-0.0011	0.0193	0.0465	-0.0035	0.0404	10.5379	49.1343	47.7114
29	4.6866	-2.1465	2.7765	5.3175	-3.9668	8.0381	-0.0177	-0.0522	-0.0162	0.0505	0.1076	0.1704	-0.1048	-0.2531	-0.0899	0.0466	-0.0116	-0.0012	0.0321	-0.0198	0.0615	-5.7217	49.7998	46.0067
30	7.293	-4.2308	1.8175	6.3017	-1.2927	3.0852	0.0122	-0.0632	-0.1605	0.1743	-0.0479	-0.2588	0.2353	0.3057	0.0357	0.0799	-0.0163	0.0161	0.0762	-0.0082	0.0528	9.5984	40.574	56.7755
31	1.86	-2.5535	2.1526	5.0847	-3.1192	2.6149	0.039	-0.0366	-0.1391	0.0478	0.0469	-0.0137	0.0634	0.0031	-0.0859	0.0427	-0.0119	0.0091	0.0571	0.0071	0.0684	2.2279	43.9434	57.4453
32	2.9572	1.415	0.0465	4.024	-1.0287	2.66	0.0056	0.3022	0.2702	-0.2544	0.064	0.1031	-0.1826	-0.0579	-0.0696	0.0574	0.0162	0.006	0.0648	-0.0016	0.0709	-6.6961	59.226	40.7408

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 14
2	X-RAY DIFFRACTION	2	A	15 - 27
3	X-RAY DIFFRACTION	3	A	28 - 47
4	X-RAY DIFFRACTION	4	A	48 - 52
5	X-RAY DIFFRACTION	5	A	53 - 63
6	X-RAY DIFFRACTION	6	A	64 - 73
7	X-RAY DIFFRACTION	7	A	74 - 85
8	X-RAY DIFFRACTION	8	A	86 - 90
9	X-RAY DIFFRACTION	9	B	1 - 4
10	X-RAY DIFFRACTION	10	B	5 - 17
11	X-RAY DIFFRACTION	11	B	18 - 23
12	X-RAY DIFFRACTION	12	B	24 - 26
13	X-RAY DIFFRACTION	13	B	31 - 43
14	X-RAY DIFFRACTION	14	B	44 - 49
15	X-RAY DIFFRACTION	15	B	50 - 82
16	X-RAY DIFFRACTION	16	B	83 - 90
17	X-RAY DIFFRACTION	17	C	1 - 6
18	X-RAY DIFFRACTION	18	C	7 - 17
19	X-RAY DIFFRACTION	19	C	18 - 31
20	X-RAY DIFFRACTION	20	C	32 - 48
21	X-RAY DIFFRACTION	21	C	49 - 53
22	X-RAY DIFFRACTION	22	C	54 - 71
23	X-RAY DIFFRACTION	23	C	72 - 81
24	X-RAY DIFFRACTION	24	C	82 - 90
25	X-RAY DIFFRACTION	25	D	1 - 5
26	X-RAY DIFFRACTION	26	D	6 - 24
27	X-RAY DIFFRACTION	27	D	25 - 42
28	X-RAY DIFFRACTION	28	D	43 - 58
29	X-RAY DIFFRACTION	29	D	59 - 64
30	X-RAY DIFFRACTION	30	D	65 - 73
31	X-RAY DIFFRACTION	31	D	74 - 84
32	X-RAY DIFFRACTION	32	D	85 - 90

-
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