PDB-4etw: Structure of the Enzyme-ACP Substrate Gatekeeper Complex Required...

ID or keywords:

Entry

Database: PDB / ID: 4etw

Title

Structure of the Enzyme-ACP Substrate Gatekeeper Complex Required for Biotin Synthesis

Components

Acyl carrier protein
Pimelyl-[acyl-carrier protein] methyl ester esterase

Keywords

HYDROLASE /

esterase

Function / homology

Function and homology information

pimelyl-[acyl-carrier protein] methyl ester esterase / biotin biosynthetic process /

carboxylic ester hydrolase activity / acyl carrier activity /

cytoplasm
Similarity search - Function

Biological species

Shigella flexneri (bacteria)

Shigella flexneri 5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Agarwal, V. / Nair, S.K.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the enzyme-acyl carrier protein (ACP) substrate gatekeeper complex required for biotin synthesis.
Authors: Agarwal, V. / Lin, S. / Lukk, T. / Nair, S.K. / Cronan, J.E.

History

Deposition	Apr 24, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 7, 2012	Group: Database references
Revision 1.2	Jul 17, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4etw.cif.gz	271.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4etw.ent.gz	230.3 KB	Display	PDB format
PDBx/mmJSON format	4etw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/et/4etw ftp://data.pdbj.org/pub/pdb/validation_reports/et/4etw	HTTPS FTP

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Related structure data

Similar structure data	2b9u-4 5inw-1 6f7y-d 4ktw-d 4tmv-2 4p0o-d 209 1pzy-2 4lrc-3 4pcb-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (7) #165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: Pimelyl-[acyl-carrier protein] methyl ester esterase

C: Pimelyl-[acyl-carrier protein] methyl ester esterase

D: Acyl carrier protein

B: Acyl carrier protein

hetero molecules

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

1

A: Pimelyl-[acyl-carrier protein] methyl ester esterase

B: Acyl carrier protein

hetero molecules

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

2

C: Pimelyl-[acyl-carrier protein] methyl ester esterase

D: Acyl carrier protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.080, 57.210, 60.950
Angle α, β, γ (deg.)	101.99, 90.10, 112.74
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 3:257 )
2	1	1	chain C and (resseq 3:257 )
1	1	2	chain D and (resseq 500:574 )
2	1	2	chain B and (resseq 500:574 )

NCS ensembles :

ID
1
2

#1: Protein	Pimelyl-[acyl-carrier protein] methyl ester esterase / Biotin synthesis protein BioH / Carboxylesterase BioH Mass: 29592.107 Da / Num. of mol.: 2 / Mutation: A82S, A243V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: bioH, SF3435, S4329 References: UniProt: Q83PW0, pimelyl-[acyl-carrier protein] methyl ester esterase
#2: Protein	Acyl carrier protein / / ACP Mass: 8514.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 5 (bacteria) / Strain: Ss046 / Gene: acpP, SFV_1114, SSON_1114 / References: UniProt: Q0T5U2
#3: Chemical	ChemComp-ZMK / methyl 7-{[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxoheptanoate Mass: 514.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₃₅N₂O₁₀PS
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.58 %

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 345708 / Num. obs: 42538

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Processing

Software

Name	Version	Classification
PHENIX	1.7.1_743	refinement
REFMAC	5.5.0109	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→35.13 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.917 / SU ML: 0.55 / σ(F): 2.16 / Phase error: 24.25 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.2359	2145	5.04 %
R_work	0.1917	-	-
obs	0.194	42538	97.83 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.223 Å² / k_sol: 0.365 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2815 Å²	-0.2009 Å²	-0.9922 Å²
2-	-	-0.5259 Å²	0.5203 Å²
3-	-	-	0.8075 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→35.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5150	0	66	223	5439

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5320
X-RAY DIFFRACTION	f_angle_d	1.195	7236
X-RAY DIFFRACTION	f_dihedral_angle_d	17.069	1940
X-RAY DIFFRACTION	f_chiral_restr	0.078	822
X-RAY DIFFRACTION	f_plane_restr	0.004	934

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1998	X-RAY DIFFRACTION	POSITIONAL
1	2	C	1998	X-RAY DIFFRACTION	POSITIONAL	0.055
2	1	D	573	X-RAY DIFFRACTION	POSITIONAL
2	2	B	573	X-RAY DIFFRACTION	POSITIONAL	0.118

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.0977	0.303	140	0.2387	2655	X-RAY DIFFRACTION	97
2.0977-2.1502	0.2446	146	0.222	2634	X-RAY DIFFRACTION	97
2.1502-2.2083	0.2689	142	0.2045	2720	X-RAY DIFFRACTION	97
2.2083-2.2733	0.2664	128	0.2129	2696	X-RAY DIFFRACTION	97
2.2733-2.3466	0.3208	133	0.2174	2653	X-RAY DIFFRACTION	97
2.3466-2.4305	0.276	141	0.2121	2696	X-RAY DIFFRACTION	98
2.4305-2.5278	0.2692	131	0.1995	2729	X-RAY DIFFRACTION	98
2.5278-2.6428	0.2714	142	0.2168	2691	X-RAY DIFFRACTION	98
2.6428-2.7821	0.2663	143	0.2118	2681	X-RAY DIFFRACTION	98
2.7821-2.9563	0.2748	129	0.2008	2721	X-RAY DIFFRACTION	98
2.9563-3.1844	0.2419	147	0.2066	2724	X-RAY DIFFRACTION	99
3.1844-3.5046	0.2436	183	0.193	2646	X-RAY DIFFRACTION	98
3.5046-4.0111	0.2315	135	0.1819	2725	X-RAY DIFFRACTION	99
4.0111-5.0512	0.1894	150	0.1546	2723	X-RAY DIFFRACTION	99
5.0512-35.135	0.1967	155	0.1818	2694	X-RAY DIFFRACTION	98

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	0.4157	0.1295	-0.2963	0.669	-0.6556	0.7154	0.1169	-0.2029	-0.2744	0.1232	-0.0874	0.024	-0.1422	0.2355	0.1428	0.1152	-0.0455	-0.021	0.1805	0.0048	0.2008	1.0978	-18.9526	29.6338
2	1.1017	-0.0105	0.3535	0.2635	0.0427	0.1211	0.1694	-0.2529	0.0393	0.2341	0.0652	0.0318	-0.2254	-0.036	0.0864	0.3941	-0.046	0.0835	0.1793	-0.0325	0.1236	-8.252	-9.5466	38.7247
3	0.0873	-0.0404	0.042	0.0199	-0.0192	0.019	0.1058	-0.0394	-0.0187	0.0984	0.0044	-0.1447	-0.0665	0.0537	0.143	0.5346	-0.2202	0.122	0.1707	-0.1491	0.3543	1.9188	-4.4701	33.6985
4	0.7067	0.0474	-1.1682	0.5857	0.1533	2.0081	0.3057	0.2179	0.4156	-0.108	0.033	0.0009	-0.8783	-0.3182	1.1054	0.4807	-0.0093	0.1661	0.0232	0.018	0.2856	-5.5477	-4.9626	21.5637
5	0.1688	0.0845	-0.0748	0.0707	0.0089	0.0996	-0.0697	0.015	-0.069	0.1466	0.1022	0.3022	-0.2036	-0.3743	0.1505	0.2969	0.2177	0.1345	0.4102	0.0351	0.2959	-24.539	-13.2025	28.8479
6	0.2725	-0.4611	0.0645	0.9982	0.2156	0.4968	-0.2292	0.1304	-0.073	0.0561	0.09	-0.0423	0.1049	-0.0888	-0.0443	0.1191	-0.1062	0.0163	0.2133	-0.0187	0.2462	-16.4158	-26.3979	24.4331
7	0.1892	0.0746	-0.338	0.0568	-0.1868	0.7735	0.2939	0.06	0.4406	0.2137	0.0029	0.0258	-0.7116	-0.235	0.3159	0.433	0.1409	0.1268	0.1012	0.0305	0.1741	-10.358	-6.5522	23.1677
8	0.3651	-0.0469	0.337	0.4446	0.188	0.9754	0.1807	0.2449	0.2213	-0.0997	0.0136	-0.0254	-0.2105	-0.0495	0.6176	0.4007	0.1279	0.1419	0.2787	0.0814	0.1463	-6.3014	-7.2325	9.0713
9	0.0144	0.0107	0.0096	0.0117	-0.0229	0.1049	0.0282	0.3576	-0.1051	-0.1737	-0.0731	-0.0371	0.1487	-0.0913	0.0011	0.1726	0.03	0.0306	0.2044	-0.0229	0.1608	-1.2845	-20.2821	16.0073
10	0.4621	-0.0911	0.1171	0.1226	0.1936	0.4724	0.0176	-0.2345	0.1814	0.1092	-0.011	0.1021	0.1639	-0.2147	-0.112	0.0928	-0.0291	0.0021	0.2464	-0.0261	0.1369	-12.1471	-22.5048	-2.3899
11	0.7552	0.2693	0.0444	0.3419	0.096	0.0274	0.0912	-0.1591	-0.0548	-0.0387	-0.1257	-0.0216	0.4326	0.2572	-0.0085	0.4743	0.0294	-0.0061	0.2828	0.0666	0.1544	-2.6555	-34.8833	1.5412
12	0.3577	-0.0861	-0.0668	0.0828	-0.1294	0.3548	0.0901	-0.1244	-0.1159	0.0553	-0.1947	0.177	0.3978	-0.1272	-0.0138	0.7024	-0.1759	0.0387	0.291	-0.0066	0.3446	-12.77	-37.3101	-5.2453
13	0.211	-0.2243	0.4827	1.3833	-0.3177	1.1343	-0.0533	0.1295	-0.0543	-0.411	-0.1197	-0.033	0.6809	-0.0492	-0.2942	0.3767	-0.026	-0.0196	0.0898	-0.0464	0.1121	-5.3567	-31.3197	-15.8463
14	0.4279	-0.1163	0.1562	0.0616	-0.0347	0.0581	-0.1	-0.0626	0.0836	0.0386	-0.0364	-0.1047	0.0786	0.225	-0.4245	0.2171	0.3326	-0.0707	0.5224	0.0762	0.1446	13.5646	-26.948	-5.595
15	0.4949	-0.2341	-0.2869	0.4608	0.1445	0.166	-0.169	-0.1099	0.1301	0.1077	-0.0866	0.032	-0.1255	0.0725	-0.1939	0.1745	-0.0707	-0.0669	0.3455	-0.0437	0.1924	5.0701	-13.5786	-3.2796
16	-0.0011	-0.0003	-0.0005	0.0095	0.0031	0.0004	0.0389	-0.0125	-0.0498	-0.0647	-0.0507	-0.0424	0.1221	0.0618	0.0563	0.6382	0.3222	0.0345	0.379	0.1793	0.2354	5.553	-34.5364	-3.014
17	0.9188	-0.2269	0.2321	0.6925	0.2629	0.2209	0.0098	0.2102	-0.0494	-0.346	-0.0376	-0.0246	0.3827	0.0038	-0.0843	0.3401	0.0378	-0.0282	0.1866	-0.0406	0.0703	-3.462	-27.3602	-22.9736
18	0.0127	0.0029	-0.0083	0.0592	-0.0306	0.0872	0.0124	0.177	0.1499	-0.1195	-0.0754	0.1539	0.0255	-0.1341	0.0126	0.1468	0.0163	-0.0417	0.1963	0.0066	0.1571	-4.6262	-18.3543	-18.349
19	0.155	-0.1154	0.1611	0.0856	-0.1194	0.1697	0.0738	0.141	0.105	-0.0684	-0.0565	0.0451	-0.0539	-0.1121	0.1102	0.1344	0.0702	-0.0484	0.3147	-0.0078	0.1992	-15.6286	-15.7286	-14.9139
20	0.0081	0.0004	-0.0018	0.0002	0.0001	0.0004	0.0487	-0.079	0.1892	0.1349	-0.0718	-0.0634	0.0126	0.1117	0.0004	0.2423	-0.0522	-0.0242	0.7632	-0.1046	0.3966	24.5228	-9.5817	5.8993
21	0.0147	-0.0027	0.0008	0.0131	-0.0078	0.0065	0.0063	0.0153	-0.0139	0.0273	0.0276	0.0074	-0.0382	0.0202	-0.0005	0.7522	0.1082	-0.2512	0.9676	0.0472	0.6454	30.9485	-16.2186	4.5734
22	0.1362	-0.0283	0.1365	0.1352	-0.0012	0.1443	0.0773	0.2811	-0.0379	-0.063	-0.0776	0.0369	0.015	0.0413	-0.0311	0.1532	-0.0751	-0.0535	0.6681	-0.0066	0.3314	29.1652	-12.1121	-5.9627
23	0.1239	0.0599	0.0363	0.0367	-0.0011	0.0519	-0.0096	0.1277	-0.0791	-0.0305	-0.0166	0.0258	0.0128	-0.0065	0.0867	0.1441	-0.0591	0.0005	0.6406	-0.1126	0.5074	15.0208	-8.3052	-0.6831
24	0.117	0.0069	0.0493	0.0114	-0.0111	0.0381	-0.1086	-0.0164	0.0347	-0.0661	-0.1459	0.0657	-0.0275	-0.013	-0.0022	0.5845	-0.045	-0.0684	0.5079	0.0815	0.5124	19.0947	-2.6889	-8.9287
25	0.0121	-0.0264	0.0062	0.0579	-0.0024	0.2224	-0.0035	-0.0622	-0.003	-0.0083	0.0025	-0.0389	-0.1296	-0.0402	-0.0044	0.3253	-0.0601	0.1187	0.4821	-0.1346	1.0417	23.4689	0.3074	0.3905
26	0.0798	0.0049	0.2447	0.0001	0.0135	0.7511	-0.2263	-0.0266	-0.2144	0.1001	-0.0112	0.0971	-0.0979	-0.051	-0.0587	0.3232	-0.0177	0.1051	0.5045	0.2318	0.7802	-37.2916	-31.7384	32.4262
27	0.0198	-0.0042	-0.0075	0.0078	0.0103	0.0122	0.0744	0.1641	-0.1323	-0.0651	-0.0685	0.0225	0.0637	-0.0015	-0	0.1995	-0.0924	0.0185	0.5688	-0.0316	0.4062	-40.2771	-26.6928	21.9875
28	0.0378	-0.0454	0.0032	0.0756	-0.0331	0.0397	-0.0194	0.0845	-0.0918	0.0233	-0.0054	-0.0198	-0.0239	-0.0365	-0.0033	0.1655	-0.0895	0.0467	0.3808	-0.045	0.5562	-27.2168	-29.8074	26.1684
29	0.0005	-0.0071	0.0047	0.194	-0.1389	0.0996	-0.1295	-0.0212	-0.0804	-0.0612	-0.0277	-0.0947	0.0888	0.0856	-0.0353	0.3415	-0.0101	0.0797	0.7685	-0.3933	0.7184	-27.4924	-35.8139	18.8193
30	0.0481	0.0841	0.0095	0.1485	0.0254	0.0531	-0.0294	0.0087	-0.0416	-0.0181	-0.0084	-0.0428	0.0602	-0.0197	-0.1211	0.3859	-0.1236	0.0985	0.2775	-0.2122	0.9322	-34.4353	-40.5054	23.405

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 3:45 )	A	3 - 45
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 46:60 )	A	46 - 60
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 61:75 )	A	61 - 75
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 76:121 )	A	76 - 121
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 122:148 )	A	122 - 148
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 149:166 )	A	149 - 166
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 167:211 )	A	167 - 211
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 212:230 )	A	212 - 230
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 231:257 )	A	231 - 257
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 3:45 )	C	3 - 45
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 46:60 )	C	46 - 60
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 61:75 )	C	61 - 75
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 76:121 )	C	76 - 121
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 122:148 )	C	122 - 148
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 149:167 )	C	149 - 167
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 168:185 )	C	168 - 185
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 186:221 )	C	186 - 221
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 222:241 )	C	222 - 241
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 242:257 )	C	242 - 257
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 500:514 )	D	500 - 514
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 515:520 )	D	515 - 520
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 521:534 )	D	521 - 534
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 535:554 )	D	535 - 554
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 555:563 )	D	555 - 563
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 564:574 )	D	564 - 574
26	X-RAY DIFFRACTION	26	( CHAIN B AND RESID 500:520 )	B	500 - 520
27	X-RAY DIFFRACTION	27	( CHAIN B AND RESID 521:534 )	B	521 - 534
28	X-RAY DIFFRACTION	28	( CHAIN B AND RESID 535:549 )	B	535 - 549
29	X-RAY DIFFRACTION	29	( CHAIN B AND RESID 550:563 )	B	550 - 563
30	X-RAY DIFFRACTION	30	( CHAIN B AND RESID 564:574 )	B	564 - 574

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