PDB-6f77: Crystal structure of the prephenate aminotransferase from Rhizobi...

ID or keywords:

Entry

Database: PDB / ID: 6f77

Title

Crystal structure of the prephenate aminotransferase from Rhizobium meliloti

Components

(Aspartate aminotransferase A) x 2

Keywords

TRANSFERASE / Prephenate aminotransferase Rhizobium meliloti

Function / homology

Function and homology information

glutamate-prephenate aminotransferase / glutamate-prephenate aminotransferase activity / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function

Biological species

Rhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.794 Å

Authors

Cobessi, D. / Giustini, C. / Graindorge, M. / Matringe, M.

Citation

Journal: Febs J. / Year: 2019
Title: Tyrosine metabolism: identification of a key residue in the acquisition of prephenate aminotransferase activity by 1 beta aspartate aminotransferase.
Authors: Giustini, C. / Graindorge, M. / Cobessi, D. / Crouzy, S. / Robin, A. / Curien, G. / Matringe, M.

History

Deposition	Dec 7, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 12, 2019	Group: Data collection / Database references Category: citation / pdbx_database_proc ...citation / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2	Jan 17, 2024	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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PDBx/mmCIF format	6f77.cif.gz	943.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6f77.ent.gz	777.3 KB	Display	PDB format
PDBx/mmJSON format	6f77.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6f77_validation.pdf.gz	489.1 KB	Display	wwPDB validaton report
Full document	6f77_full_validation.pdf.gz	503.8 KB	Display
Data in XML	6f77_validation.xml.gz	96.9 KB	Display
Data in CIF	6f77_validation.cif.gz	140.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/6f77 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/6f77	HTTPS FTP

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Related structure data

Related structure data	6f35C 6f5vSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4w5k-d 2qa3-1 6l1o-d 1asn-d 3t32-d 4dq6-d 5z0q-5 6qp2-d 1d2f-d 1bqd-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6f35C

6f5vSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aspartate aminotransferase A

B: Aspartate aminotransferase A

C: Aspartate aminotransferase A

D: Aspartate aminotransferase A

E: Aspartate aminotransferase A

F: Aspartate aminotransferase A

hetero molecules

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

1

A: Aspartate aminotransferase A

B: Aspartate aminotransferase A

hetero molecules

defined by software
Evidence: gel filtration
87.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Aspartate aminotransferase A

D: Aspartate aminotransferase A

hetero molecules

defined by software
Evidence: gel filtration
87.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Aspartate aminotransferase A

F: Aspartate aminotransferase A

hetero molecules

defined by software
Evidence: gel filtration
87.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.543, 93.008, 123.069
Angle α, β, γ (deg.)	90.00, 91.36, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Aspartate aminotransferase A / AspAT / Transaminase A Mass: 43630.609 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria) Strain: 1021 / Gene: aatA, R02325, SMc01578 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02635, aspartate transaminase
#2: Protein	Aspartate aminotransferase A / AspAT / Transaminase A Mass: 43858.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria) Strain: 1021 / Gene: aatA, R02325, SMc01578 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02635, aspartate transaminase
#3: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1616 / 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: 2.29 Å³/Da / Density % sol: 46.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 0.2 M ammonium formate, 19 % PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97931 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 1.79→48.118 Å / Num. obs: 213629 / % possible obs: 98 % / Redundancy: 2.96 % / CC_1/2: 0.995 / R_sym value: 0.094 / Net I/σ(I): 9.77
Reflection shell	Resolution: 1.79→1.9 Å / Redundancy: 2.94 % / Mean I/σ(I) obs: 2.28 / Num. unique obs: 33152 / CC_1/2: 0.729 / R_sym value: 0.577 / % possible all: 94.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6F5V

6f5v

Resolution: 1.794→48.118 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2087	10687	5 %
R_work	0.1744	-	-
obs	0.1761	213557	98.02 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.794→48.118 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17962	0	79	1616	19657

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	18718
X-RAY DIFFRACTION	f_angle_d	0.876	25532
X-RAY DIFFRACTION	f_dihedral_angle_d	11.048	11244
X-RAY DIFFRACTION	f_chiral_restr	0.05	2838
X-RAY DIFFRACTION	f_plane_restr	0.006	3342

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 (%)
1.7945-1.8148	0.3367	284	0.2939	5480	X-RAY DIFFRACTION	79
1.8148-1.8362	0.2917	347	0.245	6722	X-RAY DIFFRACTION	98
1.8362-1.8586	0.2635	352	0.2349	6800	X-RAY DIFFRACTION	99
1.8586-1.8821	0.2708	374	0.2412	6727	X-RAY DIFFRACTION	98
1.8821-1.9069	0.2816	368	0.2339	6726	X-RAY DIFFRACTION	98
1.9069-1.933	0.2837	384	0.2294	6756	X-RAY DIFFRACTION	99
1.933-1.9606	0.2944	373	0.2258	6778	X-RAY DIFFRACTION	99
1.9606-1.9899	0.2599	344	0.2217	6822	X-RAY DIFFRACTION	99
1.9899-2.021	0.2587	313	0.2108	6823	X-RAY DIFFRACTION	99
2.021-2.0541	0.2372	374	0.2025	6783	X-RAY DIFFRACTION	99
2.0541-2.0895	0.2422	340	0.2059	6808	X-RAY DIFFRACTION	99
2.0895-2.1275	0.2366	386	0.1985	6793	X-RAY DIFFRACTION	99
2.1275-2.1685	0.2233	371	0.1906	6857	X-RAY DIFFRACTION	99
2.1685-2.2127	0.2244	319	0.1891	6832	X-RAY DIFFRACTION	99
2.2127-2.2608	0.2442	368	0.1833	6817	X-RAY DIFFRACTION	99
2.2608-2.3134	0.2279	353	0.1829	6831	X-RAY DIFFRACTION	99
2.3134-2.3713	0.2303	397	0.1841	6804	X-RAY DIFFRACTION	99
2.3713-2.4354	0.2102	374	0.1766	6801	X-RAY DIFFRACTION	99
2.4354-2.5071	0.2144	348	0.1751	6861	X-RAY DIFFRACTION	99
2.5071-2.588	0.2178	344	0.173	6873	X-RAY DIFFRACTION	99
2.588-2.6805	0.2049	378	0.1694	6802	X-RAY DIFFRACTION	99
2.6805-2.7878	0.218	358	0.1713	6846	X-RAY DIFFRACTION	99
2.7878-2.9146	0.2099	368	0.1652	6816	X-RAY DIFFRACTION	99
2.9146-3.0683	0.1963	362	0.1641	6823	X-RAY DIFFRACTION	99
3.0683-3.2605	0.1931	392	0.1541	6758	X-RAY DIFFRACTION	98
3.2605-3.5121	0.1771	325	0.1537	6799	X-RAY DIFFRACTION	98
3.5121-3.8654	0.1739	339	0.1471	6824	X-RAY DIFFRACTION	98
3.8654-4.4244	0.1615	326	0.1387	6792	X-RAY DIFFRACTION	97
4.4244-5.573	0.1564	372	0.141	6826	X-RAY DIFFRACTION	98
5.573-48.1353	0.1792	354	0.1664	6890	X-RAY DIFFRACTION	97

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	0.1323	-0.257	-0.7055	0.5544	1.5426	3.489	-0.1082	0.6009	-0.1783	-0.053	0.4094	-0.1668	-0.1103	0.5553	-0.2666	0.2183	-0.0535	-0.0239	0.5885	-0.0608	0.5203	-56.7758	-14.224	-26.2645
2	1.4393	0.3991	-0.8477	0.6743	-0.4946	1.575	-0.1505	0.1436	-0.1854	-0.1235	0.083	-0.0408	0.2705	-0.0345	0.0567	0.1348	-0.0043	-0.0208	0.0606	-0.0192	0.1541	-53.0842	-37.757	-16.2985
3	3.7174	-0.2009	-0.5308	2.559	0.8106	1.797	0.0187	-0.3499	-0.0828	0.1221	-0.0088	-0.0314	0.1412	0.1513	-0.0165	0.1063	-0.0056	-0.014	0.0966	0.0166	0.0677	-46.6769	-28.2607	-1.2926
4	0.937	-0.4831	-0.4083	1.3823	0.6265	2.1575	0.051	-0.0456	0.2326	0.0143	0.016	-0.046	-0.1756	0.2234	-0.0647	0.1248	-0.034	0.0126	0.0857	-0.0302	0.1657	-38.163	-11.7968	-10.3909
5	1.4635	0.6938	-0.1399	0.7148	0.1766	0.9512	-0.0217	-0.1222	-0.0839	0.0106	0.0054	-0.0106	0.0535	0.0748	0.0192	0.1291	0.0205	-0.0161	0.063	0.011	0.1099	-45.2683	-28.2392	-5.8692
6	1.5807	0.0536	-0.5749	2.414	-1.541	3.2772	-0.0062	0.1627	-0.0103	-0.1419	0.0224	0.0744	0.0122	-0.1056	-0.0113	0.0667	-0.0046	-0.0128	0.1194	-0.0331	0.0933	-36.1044	-22.076	-31.999
7	2.8781	1.5402	-0.6965	3.7949	-0.705	4.6542	-0.1655	0.4124	-0.1527	-0.3495	0.0889	0.0015	0.3263	-0.157	0.0606	0.0638	0.0056	-0.022	0.1681	-0.0124	0.1055	-36.7129	-24.5345	-36.1793
8	1.3807	1.3598	-1.2837	2.26	-2.1023	1.964	0.2869	-0.5645	-0.358	0.3103	0.1863	0.5116	-0.1356	-0.0625	-0.3944	0.2744	0.0002	-0.0147	0.4526	0.0882	0.5098	-63.0343	-20.8133	9.3451
9	1.7117	-0.2664	-0.6359	0.6655	-0.0174	1.0801	0.0151	0.0783	0.0589	0.0028	0.0374	0.0481	-0.074	-0.1952	-0.0439	0.1243	0.0077	-0.033	0.1073	0.0306	0.111	-75.1234	-24.5699	-11.9721
10	1.8617	-0.1522	-0.3637	1.0431	-0.1871	2.7898	-0.0947	-0.5132	-0.2327	0.2945	0.0557	-0.0466	0.0306	-0.0473	0.0095	0.163	0.0329	-0.0087	0.2764	0.0829	0.1667	-82.9158	-32.7	11.3307
11	3.3781	0.6678	-1.7998	0.5005	-0.4277	1.6596	0.1383	-0.1145	0.1428	0.2071	-0.1621	0.2103	-0.1502	-0.5148	-0.0102	0.2495	0.0601	-0.1086	0.4196	0.0248	0.264	-31.9955	-35.5461	37.3625
12	2.6928	-0.7349	-1.5133	1.7016	0.7298	2.3041	0.4034	0.7033	0.2307	-0.0521	-0.1362	0.0446	-0.4662	-0.8303	-0.2321	0.2714	0.1836	0.0242	0.6145	0.0847	0.2319	-42.4572	-25.3465	27.6768
13	1.5343	-0.0853	-0.1233	3.4636	0.178	2.3475	0.2581	-0.5689	-0.2432	0.6763	-0.6006	-0.2639	0.0775	-0.1475	0.3472	0.3317	-0.1415	-0.0205	0.8362	0.1154	0.3634	-48.1964	-31.9423	53.3894
14	0.366	0.1793	-0.9295	0.7044	-0.7065	2.3076	0.5261	0.7566	-0.1909	0.2333	0.238	0.2599	-0.881	-0.4527	-0.6205	0.5126	0.2057	0.1243	1.0458	-0.1336	0.8576	-23.2009	-20.8667	13.443
15	2.676	0.4669	-1.5893	1.1222	-0.4287	1.9479	0.2475	-0.4202	0.2987	0.0272	-0.0471	0.0331	-0.2738	0.3077	-0.1686	0.1896	-0.0419	-0.0023	0.2937	-0.1223	0.181	-10.798	-29.0097	32.7262
16	2.621	0.1724	-1.2281	1.7174	-0.4929	2.9567	0.0961	0.5883	0.0327	-0.3245	-0.1376	0.1401	0.0038	-0.3521	0.0107	0.1616	0.06	-0.0238	0.3879	-0.0396	0.1665	-3.5551	-32.1012	7.9778
17	1.232	-1.1768	-2.7006	1.1968	2.8038	6.2835	0.1173	0.252	0.2248	-0.1691	0.4055	-0.3439	-0.4025	0.8399	-0.5102	0.2613	-0.0509	0.0016	0.5524	0.0079	0.4605	-7.2332	-60.6694	36.6137
18	1.7788	0.4154	-1.1479	0.7338	-0.2987	1.3969	-0.3085	0.1821	-0.3685	-0.1384	0.0847	-0.0644	0.3965	-0.0508	0.2117	0.2047	-0.015	0.0216	0.1248	-0.0218	0.226	-3.1635	-85.2356	43.8946
19	3.1996	0.0447	0.2992	2.4493	0.5017	2.3655	-0.0166	-0.2904	-0.222	0.1444	-0.11	-0.1169	0.2223	0.3201	0.1384	0.1155	0.0066	0.02	0.2231	0.0661	0.1051	3.3459	-77.5292	59.8719
20	1.806	-0.3995	-1.2499	1.6693	0.4983	2.8734	0.1252	-0.3919	0.268	0.083	-0.02	-0.0941	-0.1933	0.4109	-0.0987	0.1186	-0.0567	0.0095	0.1905	-0.0497	0.1514	11.9076	-60.314	52.3886
21	1.6254	0.6536	-1.0779	0.459	-0.6121	1.385	-0.1121	-0.2864	-0.2543	0.029	-0.0461	-0.0834	0.2205	0.298	0.1486	0.1408	0.0397	0.0003	0.1595	0.0362	0.1559	7.4102	-77.6184	51.0132
22	2.8859	0.1456	-0.6639	1.9035	-0.2954	3.2259	0.0053	0.4582	0.0678	-0.2899	-0.0502	0.1235	-0.0534	-0.2324	0.0127	0.1062	0.016	-0.0181	0.2084	0.0058	0.1037	12.4382	-65.616	26.5349
23	0.0006	-0.3858	0.2023	7.0929	-4.849	3.1895	0.2071	-0.0177	-0.2154	0.3777	0.9526	1.8405	-0.1275	-0.5388	-1.12	0.3627	0.0208	0.0923	0.5788	0.077	0.7069	-12.924	-70.604	70.9659
24	1.9504	0.0359	-0.9374	0.6062	0.0083	1.6892	-0.0069	0.1381	0.0792	-0.0426	0.0551	0.0651	-0.04	-0.2553	-0.0496	0.1475	-0.0115	-0.0418	0.1085	0.0296	0.144	-25.3537	-72.9366	49.9524
25	1.7091	0.2052	-0.8149	1.3572	0.1602	2.7151	-0.0241	-0.2449	-0.1405	0.1969	0.0211	-0.0498	0.2339	-0.0078	0.0156	0.1404	0.0099	-0.0259	0.1677	0.0448	0.1463	-32.9467	-84.1179	72.414

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 109 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 110 through 204 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 205 through 289 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 290 through 369 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 370 through 401 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 29 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 30 through 289 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 290 through 401 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 59 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 60 through 289 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 290 through 401 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 2 through 28 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 29 through 289 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 290 through 401 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 2 through 28 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 29 through 70 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 71 through 109 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 110 through 204 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 205 through 312 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 313 through 401 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 2 through 28 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 29 through 289 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 290 through 401 )

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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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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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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

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi