PDB-3kqf: 1.8 Angstrom Resolution Crystal Structure of Enoyl-CoA Hydratase ...

ID or keywords:

Entry

Database: PDB / ID: 3kqf

Title

1.8 Angstrom Resolution Crystal Structure of Enoyl-CoA Hydratase from Bacillus anthracis.

Components

Enoyl-CoA hydratase/isomerase family protein

Keywords

ISOMERASE / Enoyl-CoA Hydratase / idp02329 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

enoyl-CoA hydratase / isomerase activity
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Minasov, G. / Halavaty, A. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: 1.8 Angstrom Resolution Crystal Structure of Enoyl-CoA Hydratase from Bacillus anthracis.
Authors: Minasov, G. / Halavaty, A. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F.

History

Deposition	Nov 17, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3kqf.cif.gz	326.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3kqf.ent.gz	281.8 KB	Display	PDB format
PDBx/mmJSON format	3kqf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3kqf_validation.pdf.gz	462.8 KB	Display	wwPDB validaton report
Full document	3kqf_full_validation.pdf.gz	474.3 KB	Display
Data in XML	3kqf_validation.xml.gz	61.8 KB	Display
Data in CIF	3kqf_validation.cif.gz	89.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kq/3kqf ftp://data.pdbj.org/pub/pdb/validation_reports/kq/3kqf	HTTPS FTP

-
Related structure data

Similar structure data	5jbx-d 3myb-d 2ppy-2 3pea-2 4wcz-2 4nek-2 5jbw-1 2fw2-2 3hp0-8 3hin-4 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
Other databases	TargetDB: idp02329

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Enoyl-CoA hydratase/isomerase family protein

B: Enoyl-CoA hydratase/isomerase family protein

C: Enoyl-CoA hydratase/isomerase family protein

D: Enoyl-CoA hydratase/isomerase family protein

E: Enoyl-CoA hydratase/isomerase family protein

F: Enoyl-CoA hydratase/isomerase family protein

hetero molecules

175 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Enoyl-CoA hydratase/isomerase family protein

B: Enoyl-CoA hydratase/isomerase family protein

C: Enoyl-CoA hydratase/isomerase family protein

hetero molecules

defined by author&software
87.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Enoyl-CoA hydratase/isomerase family protein

E: Enoyl-CoA hydratase/isomerase family protein

F: Enoyl-CoA hydratase/isomerase family protein

hetero molecules

defined by author&software
87.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.747, 130.721, 73.802
Angle α, β, γ (deg.)	90.00, 114.47, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Enoyl-CoA hydratase/isomerase family protein Mass: 29096.311 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAS2374, BA_2551, GBAA2551, GBAA_2551 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 References: UniProt: Q81Q82, UniProt: A0A6L8PDF4*PLUS, enoyl-CoA hydratase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 843 / 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: 1.85 Å³/Da / Density % sol: 33.68 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Protein solution: 0.3M NaCl, 10mM HEPES, pH 7.5. Screen solution: PEG400 28%, CaCl2 0.2M, Hepes 0.1M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2009 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. all: 116373 / Num. obs: 116373 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 22.1 Å² / R_merge(I) obs: 0.091 / Net I/σ(I): 14.3
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.556 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5755 / % possible all: 100

-
Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
CRANK		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.8→29.87 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.957 / SU B: 4.048 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual Temperature Factors Refined
Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19325	5782	5 %	RANDOM
R_work	0.1555	-	-	-
all	0.15737	109827	-	-
obs	0.15737	109827	98.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 15.177 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.23 Å²	0 Å²	0.98 Å²
2-	-	0.66 Å²	-0 Å²
3-	-	-	1.38 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11812	0	7	843	12662

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	12628
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8550
X-RAY DIFFRACTION	r_angle_refined_deg	1.324	1.982	17145
X-RAY DIFFRACTION	r_angle_other_deg	0.864	3	21090
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.704	5	1689
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.082	24.991	541
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.265	15	2385
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.198	15	92
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	2002
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14417
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2319
X-RAY DIFFRACTION	r_mcbond_it	0.925	1.5	8116
X-RAY DIFFRACTION	r_mcbond_other	0.309	1.5	3330
X-RAY DIFFRACTION	r_mcangle_it	1.56	2	13117
X-RAY DIFFRACTION	r_scbond_it	2.785	3	4512
X-RAY DIFFRACTION	r_scangle_it	4.571	4.5	4028

LS refinement shell

Resolution: 1.8→1.849 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.257	399	-
R_work	0.204	7450	-
obs	-	7450	91.15 %

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	2.2962	-0.5399	0.7431	1.0691	-0.2359	2.1717	0.0387	0.3022	0.009	-0.1407	-0.02	-0.1763	0.0002	0.3202	-0.0187	0.078	-0.0157	0.051	0.1307	-0.0341	0.0774	9.3312	31.3897	-33.2673
2	4.1207	-0.8883	2.3892	0.2394	-0.4301	1.9964	-0.098	-0.0666	0.115	-0.0305	0.0996	-0.0731	-0.1288	0.1819	-0.0015	0.1404	-0.0501	0.011	0.1826	-0.0601	0.164	10.9613	39.4144	-19.4477
3	0.6112	0.0901	0.5305	1.2246	0.6783	1.896	-0.0243	0.0605	-0.1704	0.0024	0.0503	-0.1492	0.1131	0.0614	-0.026	0.0579	-0.0102	0.025	0.0386	-0.0239	0.0899	0.4925	26.0505	-24.2421
4	0.5205	-0.1267	0.1215	0.4751	0.0936	1.3801	-0.0183	0.0645	-0.1497	-0.0392	0.0132	-0.0423	0.1273	-0.0258	0.0051	0.0756	-0.0017	0.0089	0.02	-0.0252	0.063	-3.3672	25.5386	-20.7003
5	1.0002	-0.3033	-0.3087	1.293	0.6578	3.4201	0.0699	0.2166	-0.0023	-0.2218	-0.1096	0.0793	-0.0833	-0.1151	0.0397	0.1101	-0.0007	-0.0178	0.0626	-0.0159	0.0378	-16.729	41.2435	-39.6509
6	2.3921	0.2372	-0.7783	1.3682	0.2879	2.351	-0.0217	0.3032	0.1424	-0.28	0.0206	0.2642	-0.0633	-0.2985	0.0011	0.0941	-0.0157	-0.0809	0.1585	-0.0305	0.1186	-42.1381	33.73	-28.3246
7	3.1546	0.4015	-1.4528	3.2999	-0.6824	8.6025	-0.1604	0.7981	0.3028	-0.9756	-0.0971	0.042	-0.4138	-0.0729	0.2575	0.3888	0.0042	-0.0666	0.2706	0.051	0.193	-31.8451	43.4637	-35.3011
8	1.3394	0.303	-0.1905	1.3146	0.024	1.7584	-0.0523	0.1416	-0.1041	-0.2201	-0.0251	0.0032	0.1031	-0.1118	0.0774	0.0809	-0.0214	-0.0009	0.0628	-0.0474	0.0506	-29.8486	28.2611	-27.2864
9	1.2094	0.3871	-0.6526	0.3842	0.148	1.0926	-0.0449	0.0562	-0.1163	-0.0383	-0.0392	0.0335	0.0973	-0.1139	0.0842	0.0834	-0.0104	-0.0146	0.0487	-0.0363	0.0676	-24.7752	27.2991	-25.7491
10	2.9621	1.1395	-0.4481	1.6832	0.1352	1.9683	0.1103	-0.207	0.0836	0.2133	-0.2109	0.2209	0.0696	-0.3378	0.1006	0.1058	-0.0238	0.0211	0.0923	-0.0429	0.0569	-34.4786	38.1847	-1.7692
11	3.6504	0.3816	-0.7864	1.1387	0.1961	1.8793	0.015	-0.4831	-0.1757	0.2413	-0.0321	-0.0366	0.0743	0.0732	0.0171	0.1956	0.0197	-0.0015	0.1142	0.0603	0.0375	-12.8104	27.4276	12.6384
12	9.9947	0.0608	-4.1097	0.319	0.2849	2.745	0.2872	-0.072	0.2761	0.104	-0.1231	0.1027	-0.2423	-0.3247	-0.1641	0.2145	0.0432	0.0343	0.1508	-0.0063	0.0934	-23.4991	38.3909	8.8234
13	1.9629	-0.5902	-0.1027	1.0017	0.2664	1.6355	-0.0053	-0.1816	-0.2197	0.135	-0.0161	0.1515	0.1955	-0.0906	0.0215	0.1252	-0.0158	0.0178	0.0272	0.0152	0.0412	-17.4426	24.4524	0.1127
14	2.328	-0.1314	0.2672	0.6615	-0.1007	0.5824	-0.0256	-0.0719	-0.2583	0.0602	-0.028	0.0123	0.1769	-0.0422	0.0537	0.1111	-0.016	0.021	0.0065	0.0024	0.044	-18.574	24.6742	-4.8724
15	2.0081	-0.568	0.3879	1.9005	-0.1655	1.2268	-0.0432	-0.0624	-0.0921	0.1358	0.0133	-0.2321	-0.08	0.1731	0.0299	0.0734	-0.0062	-0.0263	0.0457	-0.0086	0.0683	7.4746	35.6301	-5.5874
16	1.5563	0.0468	0.6743	1.0907	-0.4773	3.5296	-0.0239	0.2357	-0.0226	-0.1214	-0.0256	-0.1992	0.0462	0.3865	0.0496	0.0709	-0.0204	0.0509	0.1231	-0.0313	0.0995	12.5273	65.7217	-28.2123
17	0.5364	-0.1394	0.8041	0.2737	-1.263	6.7727	0.0074	0.2054	-0.0747	-0.0543	0.0667	-0.05	0.2019	-0.0536	-0.0741	0.1976	-0.0338	0.0286	0.1971	-0.0787	0.144	0.7771	57.6808	-35.4355
18	1.6732	0.5647	0.9732	1.3291	0.6094	1.3473	-0.0346	0.0566	0.1357	-0.1744	0.0501	-0.0527	-0.1571	0.0607	-0.0154	0.058	-0.0154	0.0263	0.0121	-0.0039	0.0284	0.6845	71.0263	-23.851
19	1.3005	0.0996	0.4706	0.6027	-0.1124	0.6128	0.0119	-0.0405	0.1512	-0.0223	0.013	-0.0501	-0.0995	0.0426	-0.0249	0.087	-0.0127	0.0182	0.0258	-0.0148	0.0517	-4.2528	71.5298	-21.9223
20	3.7997	0.9673	0.8131	1.338	0.1781	1.4466	0.052	-0.2338	-0.1423	0.1454	-0.0972	-0.2096	0.0206	0.1573	0.0452	0.0957	-0.006	-0.0341	0.0649	0.0039	0.0707	7.7884	56.0316	-1.7665
21	2.5853	0.3559	-0.3273	1.5985	0.5298	1.7839	-0.0048	-0.4276	-0.0693	0.3645	0.0278	-0.1633	0.1639	0.1157	-0.023	0.2236	-0.0203	-0.0274	0.187	-0.0344	0.0307	-13.2543	63.2798	16.7831
22	7.6884	-0.5974	0.6379	4.0038	0.9821	2.6638	0.1453	-0.4002	-0.4658	0.5436	0.1245	-1.0429	0.4833	0.6277	-0.2698	0.3142	0.0601	-0.1127	0.2682	0.0067	0.3434	-2.9921	53.5568	10.0972
23	2.0281	0.3597	0.1844	1.3491	0.206	1.353	0.0829	-0.2	0.1666	0.0554	-0.0524	-0.1862	-0.0477	0.0724	-0.0305	0.1026	-0.0254	-0.0038	0.0646	-0.0388	0.0669	-9.1495	68.7905	4.973
24	1.7329	-0.1866	-0.2394	0.5203	0.4415	0.4397	0.0508	-0.1708	0.1699	0.0458	-0.0491	-0.0081	-0.0399	-0.019	-0.0018	0.1003	-0.0296	-0.0086	0.0406	-0.0305	0.0401	-8.4845	69.7621	-0.2902
25	3.1111	-0.4937	-0.6802	1.5886	1.271	2.6486	0.0519	-0.3303	0.0942	0.0629	-0.224	0.3265	0.0306	-0.3358	0.1721	0.097	-0.0312	0.0133	0.1141	-0.0554	0.106	-34.4781	59.0903	-1.169
26	2.7407	0.051	-1.1334	1.0638	0.0778	2.2141	0.0088	0.2836	0.0867	-0.1008	-0.0534	0.2457	-0.1192	-0.3994	0.0446	0.0866	0.0385	-0.0543	0.1168	0.0338	0.1491	-38.5065	69.6507	-27.0343
27	6.6324	0.7082	-5.2072	0.1952	-0.2338	5.9542	-0.1494	-0.2397	-0.4189	-0.0149	-0.1356	0.051	0.0997	-0.1746	0.285	0.1271	-0.0135	-0.0031	0.17	0.0123	0.2428	-39.4047	58.6954	-15.717
28	1.6816	0.0786	0.107	0.719	-0.4505	1.5237	0.0134	-0.0173	0.2878	0.0695	-0.0363	0.1167	-0.2002	-0.1328	0.0229	0.0951	0.0138	-0.0162	0.0218	-0.0126	0.1032	-28.9113	72.5654	-17.7144
29	0.7068	-0.0033	-0.4077	0.4237	0.0385	1.3617	0.0429	-0.0091	0.2415	-0.0457	-0.0139	0.0558	-0.1477	-0.0956	-0.029	0.0823	0.0046	-0.0053	0.0127	-0.0151	0.1006	-24.9019	72.4528	-14.5624
30	1.1891	-0.1126	0.3293	1.8602	-0.6213	2.2166	0.0598	0.2222	-0.031	-0.2965	0.0022	0.0303	-0.0095	0.0211	-0.062	0.1201	-0.0136	-0.0042	0.0552	-0.0126	0.0176	-13.4011	61.5996	-38.1553

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 67
2	X-RAY DIFFRACTION	2	A	68 - 100
3	X-RAY DIFFRACTION	3	A	101 - 134
4	X-RAY DIFFRACTION	4	A	135 - 204
5	X-RAY DIFFRACTION	5	A	205 - 262
6	X-RAY DIFFRACTION	6	B	1 - 67
7	X-RAY DIFFRACTION	7	B	68 - 100
8	X-RAY DIFFRACTION	8	B	101 - 134
9	X-RAY DIFFRACTION	9	B	135 - 204
10	X-RAY DIFFRACTION	10	B	205 - 262
11	X-RAY DIFFRACTION	11	C	1 - 67
12	X-RAY DIFFRACTION	12	C	68 - 100
13	X-RAY DIFFRACTION	13	C	101 - 134
14	X-RAY DIFFRACTION	14	C	135 - 204
15	X-RAY DIFFRACTION	15	C	205 - 262
16	X-RAY DIFFRACTION	16	D	1 - 67
17	X-RAY DIFFRACTION	17	D	68 - 100
18	X-RAY DIFFRACTION	18	D	101 - 134
19	X-RAY DIFFRACTION	19	D	135 - 204
20	X-RAY DIFFRACTION	20	D	205 - 262
21	X-RAY DIFFRACTION	21	E	1 - 67
22	X-RAY DIFFRACTION	22	E	68 - 100
23	X-RAY DIFFRACTION	23	E	101 - 134
24	X-RAY DIFFRACTION	24	E	135 - 204
25	X-RAY DIFFRACTION	25	E	205 - 262
26	X-RAY DIFFRACTION	26	F	1 - 67
27	X-RAY DIFFRACTION	27	F	68 - 100
28	X-RAY DIFFRACTION	28	F	101 - 134
29	X-RAY DIFFRACTION	29	F	135 - 204
30	X-RAY DIFFRACTION	30	F	205 - 262

-
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