PDB-3s0c: Transaldolase wt of Thermoplasma acidophilum

ID or keywords:

Entry

Database: PDB / ID: 3s0c

Title

Transaldolase wt of Thermoplasma acidophilum

Components

Probable transaldolase

Keywords

TRANSFERASE / ALPHA-BETA BARREL / DOMAIN SWAPPING / PROTEIN DYNAMICS / CONFORMATIONAL SELECTION

Function / homology

Function and homology information

transaldolase / transaldolase activity / aldehyde-lyase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function

Biological species

Thermoplasma acidophilum (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Lehwess-Litzmann, A. / Neumann, P. / Parthier, C. / Tittmann, K.

Citation

Journal: Nat.Chem.Biol. / Year: 2011
Title: Twisted Schiff base intermediates and substrate locale revise transaldolase mechanism.
Authors: Lehwess-Litzmann, A. / Neumann, P. / Parthier, C. / Ludtke, S. / Golbik, R. / Ficner, R. / Tittmann, K.

History

Deposition	May 13, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 24, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 7, 2011	Group: Database references
Revision 1.2	Oct 5, 2011	Group: Database references
Revision 1.3	Sep 4, 2019	Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.4	Sep 13, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s0c.cif.gz	473.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3s0c.ent.gz	392.9 KB	Display	PDB format
PDBx/mmJSON format	3s0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3s0c_validation.pdf.gz	478.6 KB	Display	wwPDB validaton report
Full document	3s0c_full_validation.pdf.gz	511.7 KB	Display
Data in XML	3s0c_validation.xml.gz	54.7 KB	Display
Data in CIF	3s0c_validation.cif.gz	78.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s0/3s0c ftp://data.pdbj.org/pub/pdb/validation_reports/s0/3s0c	HTTPS FTP

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Related structure data

Related structure data	3s1uC 3s1vC 3s1wC 3s1xC 1wx0S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6ys0-1 6yrh-1 3s1x-1 3s1w-1 4xz9-1 6yrm-1 6yr3-1 3s1v-1 6yre-1 5zol-d 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

Deposited unit

A: Probable transaldolase

B: Probable transaldolase

C: Probable transaldolase

D: Probable transaldolase

E: Probable transaldolase

hetero molecules

123 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Probable transaldolase

B: Probable transaldolase

C: Probable transaldolase

D: Probable transaldolase

E: Probable transaldolase

hetero molecules

A: Probable transaldolase

B: Probable transaldolase

C: Probable transaldolase

D: Probable transaldolase

E: Probable transaldolase

hetero molecules

defined by author&software
245 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	149.044, 172.024, 100.271
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-290- HOH
2	1	C-549- HOH

#1: Protein	Probable transaldolase Mass: 24494.545 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165 Gene: Ta0616, tal / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q9HKI3, transaldolase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 972 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	AUTHORS STATE THAT THE GENE WAS CLONED FROM AUTHENTIC DNA DERIVED FROM WILD-TYPE THERMOPLASMA ACIDOPHILUM.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.12 %
Crystal grow	Temperature: 291 K / Method: hanging drop / pH: 4.5 Details: PEG 6000, GOL, pH 4.5, hanging drop, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.91841 Å

Detector

Type: MARRESEARCH / Detector: CCD / Date: Feb 5, 2009

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.91841 Å / Relative weight: 1

Reflection

Resolution: 1.78→34.199 Å / Num. all: 121135 / Num. obs: 121135 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.03 % / R_merge(I) obs: 0.039 / Net I/σ(I): 21.32

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.78-1.83		0.438	2.61	1	96.3
1.83-1.88		0.405	3.14	1	99.8
1.88-1.93		0.32	4.74	1	96.9
1.93-1.99		0.253	5.32	1	99.4
1.99-2.06		0.165	7.53	1	99.9
2.06-2.13		0.129	10.24	1	97.9
2.13-2.21		0.094	12.48	1	99.9
2.21-2.3		0.1	14.06	1	95.3
2.3-2.4		0.062	18.31	1	99.7
2.4-2.52		0.052	22.11	1	99.2
2.52-2.65		0.041	26.79	1	99.7
2.65-2.81		0.037	30.57	1	99.1
2.81-3.01		0.029	36.73	1	99.9
3.01-3.25		0.027	41.37	1	99.3
3.25-3.56		0.025	45.65	1	98.9
3.56-3.98		0.024	49.51	1	98.1
3.98-4.6		0.022	56.86	1	99.4
4.6-5.63		0.021	57.09	1	99.5
5.63-7.96		0.019	57.03	1	99.3
	7.96	0.016	57.7	1	85.4

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Processing

Software

Name	Version	Classification
XSCALE		data processing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.1	data extraction
MAR345dtb		data collection
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1WX0

1wx0

Resolution: 1.78→34.191 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.51 / σ(F): 1.99 / Phase error: 22.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2291	6055	5 %
R_work	0.1945	-	-
obs	0.1962	121119	98.54 %
all	-	121120	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.783 Å² / k_sol: 0.353 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.2288 Å²	-0 Å²	-0 Å²
2-	-	-5.3163 Å²	-0 Å²
3-	-	-	-2.9125 Å²

Refine analyze

Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.25 Å

Refinement step

Cycle: LAST / Resolution: 1.78→34.191 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8540	0	6	972	9518

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9221
X-RAY DIFFRACTION	f_angle_d	1.108	12522
X-RAY DIFFRACTION	f_dihedral_angle_d	12.944	3450
X-RAY DIFFRACTION	f_chiral_restr	0.071	1526
X-RAY DIFFRACTION	f_plane_restr	0.007	1586

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 (%)
1.78-1.8002	0.3006	192	0.2784	3651	X-RAY DIFFRACTION	95
1.8002-1.8214	0.3039	197	0.2729	3735	X-RAY DIFFRACTION	97
1.8214-1.8436	0.284	202	0.2538	3837	X-RAY DIFFRACTION	100
1.8436-1.8669	0.2927	204	0.2731	3887	X-RAY DIFFRACTION	100
1.8669-1.8915	0.3121	201	0.2971	3812	X-RAY DIFFRACTION	99
1.8915-1.9174	0.4113	194	0.3898	3676	X-RAY DIFFRACTION	96
1.9174-1.9448	0.3652	199	0.2978	3798	X-RAY DIFFRACTION	98
1.9448-1.9738	0.2626	202	0.2441	3827	X-RAY DIFFRACTION	99
1.9738-2.0047	0.2362	203	0.1943	3859	X-RAY DIFFRACTION	100
2.0047-2.0375	0.2267	203	0.1867	3862	X-RAY DIFFRACTION	100
2.0375-2.0727	0.2518	199	0.2063	3778	X-RAY DIFFRACTION	97
2.0727-2.1104	0.2651	200	0.2059	3801	X-RAY DIFFRACTION	99
2.1104-2.1509	0.2393	203	0.1799	3846	X-RAY DIFFRACTION	100
2.1509-2.1948	0.2016	205	0.1784	3904	X-RAY DIFFRACTION	100
2.1948-2.2426	0.2864	199	0.216	3776	X-RAY DIFFRACTION	98
2.2426-2.2947	0.3207	191	0.2626	3633	X-RAY DIFFRACTION	93
2.2947-2.3521	0.2556	201	0.1932	3815	X-RAY DIFFRACTION	99
2.3521-2.4157	0.2088	205	0.1796	3900	X-RAY DIFFRACTION	100
2.4157-2.4867	0.2277	205	0.1806	3886	X-RAY DIFFRACTION	100
2.4867-2.567	0.2349	203	0.1783	3852	X-RAY DIFFRACTION	99
2.567-2.6587	0.1894	203	0.1753	3867	X-RAY DIFFRACTION	100
2.6587-2.7651	0.2254	203	0.1754	3859	X-RAY DIFFRACTION	99
2.7651-2.8909	0.1898	204	0.1738	3882	X-RAY DIFFRACTION	100
2.8909-3.0432	0.2258	206	0.179	3903	X-RAY DIFFRACTION	100
3.0432-3.2337	0.1901	205	0.1817	3890	X-RAY DIFFRACTION	99
3.2337-3.4832	0.2081	202	0.183	3842	X-RAY DIFFRACTION	99
3.4832-3.8333	0.2254	205	0.18	3899	X-RAY DIFFRACTION	99
3.8333-4.387	0.1975	206	0.1581	3908	X-RAY DIFFRACTION	99
4.387-5.5234	0.1878	208	0.1681	3964	X-RAY DIFFRACTION	99
5.5234-34.1969	0.2441	205	0.2216	3915	X-RAY DIFFRACTION	95

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	4.3604	0.6732	-0.9796	2.414	0.3579	2.9826	-0.1803	0.256	-1.1584	0.0106	-0.0002	-0.1841	1.1901	-0.0752	0.1738	0.4808	-0.0226	0.0439	0.113	-0.1881	0.2965	6.3904	-71.3372	-1.6363
2	1.3244	-0.0635	-0.3854	1.5372	0.3697	1.2259	0.1036	0.2973	-0.0731	-0.2399	-0.0837	-0.3116	0.011	0.1626	-0.0283	0.2602	0.0448	0.0655	0.278	0.01	0.2125	17.889	-30.2168	-9.8243
3	1.6287	-0.0891	0.2464	1.9309	-0.5449	2.4107	0.098	0.3026	0.3644	-0.0708	-0.0571	-0.2575	-0.307	0.0872	-0.0141	0.2677	0.0444	0.0373	0.2002	0.0874	0.2427	-10.2669	-5.0057	10.4545
4	0.8352	0.6824	-0.3797	1.1329	-0.2906	0.8932	-0.0115	0.0124	0.2951	0.067	0.0031	0.1562	-0.1089	-0.1131	0.0077	0.0498	0.0283	-0.0293	0.2359	0.0198	0.2385	-39.1958	-29.0122	31.3992
5	3.0243	3.2504	-0.4438	6.1243	-1.9267	2.1267	-0.0233	-0.2466	-0.3271	0.0645	-0.1648	-0.0192	0.2242	-0.0691	0.1612	0.1802	-0.1723	0.109	0.1848	-0.0832	0.3709	-28.8076	-70.609	24.1244
6	1.1322	-0.2027	-0.3389	0.9973	0.7801	2.6299	-0.1445	0.3949	-0.8081	-0.0172	-0.0776	0.0416	1.0144	0.1147	0.2	1.013	-0.0058	0.249	0.4276	-0.2026	0.5879	11.9392	-75.1415	-11.0073
7	6.4673	4.4949	-3.1025	6.0615	-1.6887	2.7727	-0.04	0.3072	-0.178	-0.8871	-0.0692	-0.6601	-0.2327	0.3612	0.09	0.3825	0.142	0.1353	0.4818	0.083	0.233	20.962	-21.5578	-16.8795
8	1.5545	-0.5062	0.0976	0.2006	-0.3371	2.6547	0.0179	0.0529	0.4935	-0.403	-0.0041	-0.1173	-0.8103	-0.2083	-0.0175	0.4858	0.0664	0.0009	0.1556	0.0749	0.3074	-17.531	3.9788	10.7297
9	1.6052	0.3536	0.0693	1.6433	-0.8945	1.9537	0.1724	-0.409	0.4074	0.0845	0.0259	0.4438	-0.0863	-0.3149	-0.1994	0.1141	0.0338	-0.0225	0.4033	-0.0668	0.3315	-49.5373	-31.6695	33.4864
10	1.9742	0.3752	0.5224	2.9301	-0.0398	1.0166	0.0108	0.0677	-0.4423	0.0696	-0.0803	-0.437	0.3472	-0.1376	0.0781	0.341	-0.2117	0.0517	0.3538	-0.0949	0.6221	-31.5795	-79.4671	20.1212
11	1.2119	-0.0739	-0.5043	1.1304	-0.1758	1.1595	-0.0539	0.285	-0.1984	-0.3465	-0.0502	-0.0618	0.3074	-0.0662	0.0604	0.1972	0.0161	0.0182	0.1617	-0.0786	0.1221	9.0331	-56.2303	-2.4626
12	1.0081	-0.0369	-0.2748	1.3439	0.207	0.9718	0.1196	0.2387	0.1451	-0.2329	-0.0795	-0.0153	-0.1996	-0.0324	-0.0274	0.1743	0.0367	0.0014	0.1717	0.0252	0.1155	7.458	-23.2905	-0.8097
13	0.5507	0.0031	-0.2029	1.1102	0.1048	0.7828	0.0156	0.0624	0.0963	-0.0835	0.0007	0.1572	-0.1062	-0.1168	-0.0238	0.1584	0.0384	-0.0122	0.1606	0.0222	0.1598	-18.4234	-15.5014	18.1917
14	0.722	0.5395	-0.1373	1.3961	0.0605	0.7097	-0.0211	-0.0014	0.0241	-0.0672	0.0211	0.2825	0.0553	-0.2267	0.0201	0.0779	-0.0207	-0.0391	0.2008	0.0132	0.1741	-32.2798	-43.5451	28.6534
15	0.7429	-0.5726	-0.559	0.651	0.1432	0.8061	-0.1222	0.2984	-0.6108	-0.0927	-0.146	0.3341	0.4007	-0.3603	0.0976	0.0866	-0.2388	-0.0429	-0.0989	-0.2298	0.3187	-15.2121	-68.5193	16.0014
16	1.444	-0.1699	0.0709	1.4257	-0.0029	1.8536	-0.0106	-0.1396	-0.7383	0.2468	-0.0099	0.5848	0.7263	-0.6476	0.0009	0.4043	-0.1122	0.0409	0.2585	-0.0445	0.5763	-10.5564	-82.64	21.5649
17	1.5625	-0.594	-0.4916	3.1631	1.0141	2.2892	-0.113	0.4906	-0.5947	-0.3226	0.0707	-0.3301	0.7637	0.4287	-0.012	0.3655	0.1119	0.0505	0.3775	-0.1278	0.321	24.2794	-61.5987	-6.1776
18	2.1626	-0.1	-0.6501	1.0642	0.1321	1.2834	0.1297	0.4584	0.3195	-0.5173	-0.0257	-0.4223	-0.3418	0.3664	-0.0551	0.3736	-0.0485	0.0912	0.2697	0.0621	0.2491	18.1837	-10.9164	-2.7796
19	0.7938	0.2925	0.1804	1.661	-0.7006	1.7627	-0.0763	0.0315	0.4577	0.2394	0.0413	0.3723	-0.7962	-0.2729	0.0492	0.3033	0.0932	-0.0156	0.2441	-0.0194	0.2986	-22.0223	-1.7941	26.8504
20	1.6186	-0.4188	0.3064	2.1222	0.2624	2.1336	-0.1228	-0.3744	0.1637	0.1932	0.0257	0.8269	-0.221	-1.096	0.0988	0.1788	-0.0363	0.0148	0.4521	0.0181	0.2912	-41.4991	-46.9081	42.045

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1:33)
2	X-RAY DIFFRACTION	2	CHAIN B AND (RESID 1:33)
3	X-RAY DIFFRACTION	3	CHAIN C AND (RESID 1:33)
4	X-RAY DIFFRACTION	4	CHAIN D AND (RESID 1:33)
5	X-RAY DIFFRACTION	5	CHAIN E AND (RESID 1:33)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 34:55)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 34:55)
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 34:55)
9	X-RAY DIFFRACTION	9	CHAIN D AND (RESID 34:55)
10	X-RAY DIFFRACTION	10	CHAIN E AND (RESID 34:55)
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESID 56:198)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 56:198)
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESID 56:198)
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESID 56:198)
15	X-RAY DIFFRACTION	15	CHAIN E AND (RESID 56:198)
16	X-RAY DIFFRACTION	16	CHAIN A AND (RESID 199:230)
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 199:230)
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESID 199:230)
19	X-RAY DIFFRACTION	19	CHAIN D AND (RESID 199:230)
20	X-RAY DIFFRACTION	20	CHAIN E AND (RESID 199:230)

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-Basic information

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-Download

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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

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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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