PDB-5kod: Crystal Structure of GH3.5 Acyl Acid Amido Synthetase from Arabid...

ID or keywords:

Entry

Database: PDB / ID: 5kod

Title

Crystal Structure of GH3.5 Acyl Acid Amido Synthetase from Arabidopsis thaliana

Components

Indole-3-acetic acid-amido synthetase GH3.5

Keywords

LIGASE / ANL / adenylating enzyme / acyl acid amido synthetase / adenylation ligase

Function / homology

Function and homology information

indole-3-acetic acid amido synthetase activity / positive regulation of camalexin biosynthetic process / camalexin biosynthetic process / : / acid-amino acid ligase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / response to auxin / cytoplasm
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.202 Å

Authors

Jez, J.M. / Westfall, C.S. / Zubieta, C.

Funding support

United States, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Arabidopsis thaliana GH3.5 acyl acid amido synthetase mediates metabolic crosstalk in auxin and salicylic acid homeostasis.
Authors: Westfall, C.S. / Sherp, A.M. / Zubieta, C. / Alvarez, S. / Schraft, E. / Marcellin, R. / Ramirez, L. / Jez, J.M.

History

Deposition	Jun 30, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 30, 2016	Group: Database references
Revision 1.2	Dec 14, 2016	Group: Database references
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kod.cif.gz	918 KB	Display	PDBx/mmCIF format
PDB format	pdb5kod.ent.gz	764.2 KB	Display	PDB format
PDBx/mmJSON format	5kod.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kod_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5kod_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5kod_validation.xml.gz	89.8 KB	Display
Data in CIF	5kod_validation.cif.gz	127.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/5kod ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5kod	HTTPS FTP

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Related structure data

Related structure data	4eqlS S: Starting model for refinement
Similar structure data	4l39-2 4eq4-1 4b2g-2 4epl-d 5hyo-d 3zxu-1 5cgt-d 3gpl-1 2q6d-1 6cgt-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

4eqlS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Indole-3-acetic acid-amido synthetase GH3.5

B: Indole-3-acetic acid-amido synthetase GH3.5

C: Indole-3-acetic acid-amido synthetase GH3.5

D: Indole-3-acetic acid-amido synthetase GH3.5

hetero molecules

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

1

A: Indole-3-acetic acid-amido synthetase GH3.5

hetero molecules

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

2

B: Indole-3-acetic acid-amido synthetase GH3.5

hetero molecules

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

3

C: Indole-3-acetic acid-amido synthetase GH3.5

hetero molecules

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

4

D: Indole-3-acetic acid-amido synthetase GH3.5

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.609, 143.523, 102.322
Angle α, β, γ (deg.)	90.00, 114.72, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Indole-3-acetic acid-amido synthetase GH3.5 / Auxin-responsive GH3-like protein 5 / AtGH3-5 Mass: 69358.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GH3.5, At4g27260, M4I22.70 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) References: UniProt: O81829, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Chemical	ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID Mass: 175.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₉NO₂ / Comment: hormone*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1001 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.15 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 20% PEG-8000 0.1 M N-cyclohexyl-2-aminoethanesulfonic acid, pH 9.5 2 mM MgCl2 5 mM tris(2-carboxyethyl)phosphine 5 mM IAA 5 mM AMP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.2→42.2 Å / Num. obs: 108566 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Redundancy: 2.26 % / R_sym value: 0.093 / Net I/σ(I): 11.2

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4EQL

4eql

Resolution: 2.202→42.164 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2447	5419	4.99 %
R_work	0.2048	-	-
obs	0.2068	108566	89.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.202→42.164 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18129	0	154	1001	19284

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	18787
X-RAY DIFFRACTION	f_angle_d	1.167	25519
X-RAY DIFFRACTION	f_dihedral_angle_d	16.214	7073
X-RAY DIFFRACTION	f_chiral_restr	0.044	2876
X-RAY DIFFRACTION	f_plane_restr	0.005	3240

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 (%)
2.2019-2.2269	0.3105	109	0.2722	2073	X-RAY DIFFRACTION	54
2.2269-2.2531	0.3342	143	0.2607	2759	X-RAY DIFFRACTION	73
2.2531-2.2805	0.3113	175	0.255	3258	X-RAY DIFFRACTION	84
2.2805-2.3094	0.3067	185	0.2684	3594	X-RAY DIFFRACTION	95
2.3094-2.3398	0.3682	177	0.297	3350	X-RAY DIFFRACTION	87
2.3398-2.3718	0.3717	181	0.2855	3371	X-RAY DIFFRACTION	88
2.3718-2.4057	0.2613	197	0.2351	3744	X-RAY DIFFRACTION	98
2.4057-2.4416	0.2853	195	0.2226	3770	X-RAY DIFFRACTION	98
2.4416-2.4798	0.2662	196	0.2312	3734	X-RAY DIFFRACTION	98
2.4798-2.5204	0.3053	203	0.2233	3749	X-RAY DIFFRACTION	98
2.5204-2.5639	0.2834	200	0.2163	3772	X-RAY DIFFRACTION	98
2.5639-2.6105	0.2388	199	0.2242	3783	X-RAY DIFFRACTION	99
2.6105-2.6607	0.2781	90	0.2284	1748	X-RAY DIFFRACTION	93
2.6607-2.715	0.4051	32	0.2892	614	X-RAY DIFFRACTION	73
2.715-2.774	0.3315	163	0.2727	3163	X-RAY DIFFRACTION	82
2.774-2.8385	0.2896	193	0.2186	3720	X-RAY DIFFRACTION	97
2.8385-2.9095	0.2677	200	0.2124	3760	X-RAY DIFFRACTION	99
2.9095-2.9882	0.2687	198	0.2088	3802	X-RAY DIFFRACTION	99
2.9882-3.0761	0.2557	198	0.2059	3772	X-RAY DIFFRACTION	99
3.0761-3.1753	0.2547	195	0.1997	3797	X-RAY DIFFRACTION	98
3.1753-3.2888	0.2288	198	0.1973	3766	X-RAY DIFFRACTION	98
3.2888-3.4204	0.2169	202	0.1826	3793	X-RAY DIFFRACTION	98
3.4204-3.576	0.2416	199	0.1875	3740	X-RAY DIFFRACTION	98
3.576-3.7644	0.1973	196	0.1721	3760	X-RAY DIFFRACTION	98
3.7644-4.0001	0.2245	196	0.1698	3739	X-RAY DIFFRACTION	97
4.0001-4.3087	0.1959	193	0.158	3766	X-RAY DIFFRACTION	97
4.3087-4.7417	0.1856	197	0.1571	3744	X-RAY DIFFRACTION	98
4.7417-5.4266	0.1853	201	0.1707	3807	X-RAY DIFFRACTION	98
5.4266-6.8323	0.2274	202	0.2099	3837	X-RAY DIFFRACTION	99
6.8323-42.1718	0.2323	206	0.2226	3862	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	2.6883	0.5466	0.253	1.6233	-0.461	0.7868	-0.1488	-0.2403	0.414	0.2286	-0.0306	-0.1541	-0.2604	0.0936	0.0899	0.4033	-0.0228	-0.045	0.2527	-0.0501	0.2013	36.558	111.0923	66.4659
2	0.8589	0.3449	0.195	1.0526	-0.0392	0.9174	0.0202	-0.0308	-0.0142	0.0864	0.0096	0.0276	0.0472	-0.0436	-0.0356	0.2542	0.0429	-0.003	0.1824	0.0046	0.1496	20.7064	92.5007	59.1341
3	1.683	-0.2793	0.0874	1.7724	0.4439	2.819	0.076	0.1726	-0.0551	-0.3078	-0.0561	-0.1645	0.1063	0.1429	-0.0177	0.3373	0.0488	0.0387	0.1916	0.0157	0.2321	37.5996	79.7506	38.7488
4	4.9022	1.0724	0.2595	2.1725	0.4925	1.0813	-0.0613	0.5433	-0.3565	0.0664	0.1027	-0.0901	0.3891	0.2415	-0.0855	0.3153	0.0515	0.0744	0.2084	-0.0695	0.2608	13.4168	84.2668	87.2626
5	2.9541	-2.2844	-0.4251	1.9822	0.9767	1.8049	-0.0837	-0.3443	0.3433	-0.0253	0.2353	-0.4398	-0.1612	0.3128	-0.1612	0.1922	-0.0171	0.0058	0.2471	-0.022	0.28	16.1077	101.5266	93.9808
6	1.884	-0.4112	-0.2999	2.6422	-0.1272	1.1434	-0.0338	0.3357	-0.1524	-0.2173	-0.0876	0.1616	0.0957	-0.143	0.117	0.2298	-0.0344	0.0352	0.2865	-0.0745	0.1626	-6.7401	91.7688	82.6995
7	2.7805	-0.3142	-0.6942	0.8456	0.2384	1.0657	0.0565	0.5595	0.1096	-0.1414	-0.0867	0.0654	-0.0438	-0.2877	0.0351	0.2395	-0.002	-0.0025	0.3177	0.0034	0.178	-16.1525	103.2895	84.3771
8	3.6536	-1.0889	-0.2622	1.9171	0.2597	2.1974	-0.204	-0.481	-0.2296	0.4063	0.0497	-0.0812	0.1336	0.0097	0.0604	0.2853	0.0323	0.0499	0.2093	0.0008	0.2192	3.5366	86.4844	101.3604
9	2.1747	-0.5973	-0.6687	1.8629	0.6314	0.95	-0.2599	-0.2928	-0.1068	0.2028	0.1525	-0.0785	0.1728	0.1047	0.1225	0.2646	0.045	0.0142	0.1845	0.0159	0.1677	4.2356	90.0539	101.953
10	2.6131	-0.0875	0.5381	2.903	1.0773	2.6677	-0.0215	-0.1844	0.2732	0.6255	0.0724	-0.1835	0.1718	0.088	-0.0417	0.2788	0.0273	-0.0503	0.189	-0.0148	0.1847	-9.0378	118.1195	116.3638
11	1.6529	-0.5978	-1.3616	2.2341	1.5288	2.6688	-0.0209	0.0672	0.0736	-0.0266	0.0738	-0.1616	-0.142	-0.0076	-0.082	0.2063	0.0274	-0.0364	0.137	0.0056	0.1416	-9.0847	118.0017	106.6177
12	1.7316	0.518	-0.7291	2.8918	-1.5156	3.8732	-0.0633	-0.1365	-0.2216	0.5399	0.1063	-0.2074	0.3332	0.0826	-0.0281	0.3917	0.0239	-0.082	0.2023	-0.0362	0.1872	-13.6452	108.8295	118.3718
13	1.1689	-4.5208	-4.4443	2.0001	1.9998	2.0002	-0.7208	-2.1732	1.9907	3.4351	-0.2613	-1.742	-1.6732	0.883	0.9671	0.8682	0.0921	-0.2924	0.4787	0.0616	0.3231	3.0417	119.1972	92.0036
14	2.071	0.5373	0.5496	0.813	0.2714	0.9187	0.0483	0.1175	-0.098	0.0091	0.0504	-0.0686	0.103	0.1051	-0.1167	0.2685	0.0262	-0.0016	0.1574	-0.05	0.2041	-45.4958	63.0214	83.1774
15	2.0641	-0.4781	0.0252	0.2731	0.4947	0.9809	0.0965	0.0882	-0.668	-0.0414	0.0659	-0.589	0.2572	0.2048	-0.1802	0.4745	0.0526	-0.091	0.2829	-0.1062	0.487	-31.4838	53.8279	90.3216
16	3.9405	-1.1496	0.1962	1.1064	-0.7933	1.6425	0.2881	-0.4744	-0.5124	-0.1336	-0.1137	0.0454	0.248	0.3788	-0.1435	0.3395	0.0523	-0.0968	0.4114	-0.0734	0.4104	-15.5291	58.8926	103.5606
17	1.5889	-0.1504	0.7351	0.1257	-0.038	1.3788	0.0667	-0.1194	0.2312	-0.0798	-0.0211	-0.0183	-0.1003	0.0836	-0.0948	0.2675	-0.0095	-0.018	0.1691	-0.0583	0.2767	-42.0566	75.1314	91.2725
18	1.4675	0.1356	0.2877	2.2681	0.0729	4.0131	0.0204	-0.0109	-0.1379	0.4208	0.1819	-0.2099	0.2288	-0.0556	-0.1835	0.3625	0.0349	-0.077	0.1702	-0.0235	0.3035	-46.1144	65.7723	119.3494
19	2.3651	-0.1332	-1.4623	4.1666	1.5083	2.2049	0.4065	0.1841	0.1866	0.1858	-0.2234	0.1506	-0.115	-0.0264	-0.2884	0.428	0.0757	-0.117	0.3315	-0.0579	0.3477	-44.6118	78.5439	121.7385
20	1.6312	0.2571	0.8014	0.794	-0.4051	1.4373	0.008	-0.3082	-0.1592	0.1844	0.1224	0.264	0.0528	-0.4476	-0.1325	0.2791	0.0451	0.0747	0.3909	0.0601	0.3035	-24.6765	107.1186	44.2625
21	1.2159	0.4084	0.0166	1.0761	-0.4569	0.7107	0.0069	-0.1006	0.0376	0.0674	0.0497	0.0954	-0.0546	-0.0652	-0.0382	0.2392	0.0469	0.0028	0.224	0.002	0.16	-4.876	117.4454	37.2926
22	1.2803	-0.039	0.2764	1.77	-1.0973	2.8628	-0.1221	-0.2221	-0.3948	0.0719	0.1797	0.1577	0.1456	-0.2549	-0.119	0.2539	0.017	0.0123	0.2519	0.1107	0.262	-18.5307	94.7379	41.1572
23	1.5147	-0.2124	-0.5361	2.0315	1.1837	2.7179	-0.034	0.1748	-0.2646	-0.0533	0.0365	0.0193	0.2584	-0.0433	-0.0091	0.2467	0.0003	-0.0416	0.1883	-0.0179	0.2298	-8.8182	103.1639	11.1269
24	2.0903	-0.4655	-0.1066	3.9863	0.7289	2.8274	0.0905	0.0684	-0.1282	0.1738	-0.0757	0.0775	0.0896	-0.1566	0.0352	0.2098	-0.0389	-0.0621	0.1708	-0.0202	0.2357	-6.8454	106.3642	13.2821

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 18 through 91 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 92 through 446 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 447 through 608 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 16 through 66 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 67 through 123 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 124 through 160 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 161 through 347 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 348 through 396 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 397 through 459 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 460 through 512 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 513 through 552 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 553 through 602 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 603 through 604 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 16 through 161 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 162 through 206 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 207 through 302 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 303 through 446 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 447 through 552 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 553 through 601 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 16 through 161 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 162 through 401 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 402 through 446 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 447 through 573 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 574 through 606 )

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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

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+About Yorodumi

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-Aug 12, 2020. Covid-19 info

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Download

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Validation report

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi