PDB-3pzj: Crystal structure of a probable acetyltransferases (GNAT family) ...

ID or keywords:

Entry

Database: PDB / ID: 3pzj

Title

Crystal structure of a probable acetyltransferases (GNAT family) from Chromobacterium violaceum ATCC 12472

Components

Probable acetyltransferases

Keywords

TRANSFERASE / MCSG / PSI-2 /

Structural Genomics /

Protein Structure Initiative / Midwest Center for Structural Genomics / GNAT family member / acetylotransferase

Function / homology

Function and homology information

N-acetyltransferase activity /

Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function

Biological species

Chromobacterium violaceum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Nocek, B. / Stein, A. / Bigelow, L. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of a probable acetyltransferases (GNAT family) from Chromobacterium violaceum ATCC 12472
Authors: Nocek, B. / Stein, A. / Bigelow, L. / Feldmann, B. / Joachimiak, A.

History

Deposition	Dec 14, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pzj.cif.gz	162.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3pzj.ent.gz	137 KB	Display	PDB format
PDBx/mmJSON format	3pzj.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/pz/3pzj ftp://data.pdbj.org/pub/pdb/validation_reports/pz/3pzj	HTTPS FTP

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Related structure data

Similar structure data	3fmn-d 5r9z-d 5r9d-d 5r91-d 6so2-d 5r9l-d 5r9q-d 5ci6-2 6sfj-d 2dd9-2 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: apc67522.3

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: Probable acetyltransferases

B: Probable acetyltransferases

hetero molecules

46.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.665, 67.434, 85.271
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Probable acetyltransferases Mass: 23344.809 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_1740 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: Q7NX87, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.99 Å³/Da / Density % sol: 38.22 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 35% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. all: 32410 / Num. obs: 32081 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / B_iso Wilson estimate: 39.2 Å² / R_merge(I) obs: 0.071 / Net I/σ(I): 30.1
Reflection shell	Resolution: 1.85→1.92 Å / % possible all: 99.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
SHELX		model building
ARP/wARP		model building
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.85→40 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.932 / SU B: 7.298 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.153 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24407	1615	5.1 %	RANDOM
R_work	0.19492	-	-	-
all	0.198	31926	-	-
obs	0.19745	30311	98.45 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 27.458 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	0 Å²	0 Å²
2-	-	0.26 Å²	0 Å²
3-	-	-	-0.16 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2909	0	6	137	3052

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.021	3035
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2031
X-RAY DIFFRACTION	r_angle_refined_deg	1.923	1.927	4136
X-RAY DIFFRACTION	r_angle_other_deg	1.032	3	4864
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.161	5	391
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.992	22.109	147
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.665	15	429
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.714	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.131	0.2	444
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	3511
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	718
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.146	1.5	1910
X-RAY DIFFRACTION	r_mcbond_other	0.385	1.5	779
X-RAY DIFFRACTION	r_mcangle_it	1.842	2	3010
X-RAY DIFFRACTION	r_scbond_it	3.093	3	1125
X-RAY DIFFRACTION	r_scangle_it	4.51	4.5	1119
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.851→1.899 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	104	-
R_work	0.234	2194	-
obs	-	-	97.75 %

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	0.0145	0.3207	0.0654	8.9831	1.7634	0.3597	-0.0768	-0.0186	0.0101	-0.7979	0.1724	-0.1188	-0.1916	0.0201	-0.0956	0.2235	-0.0352	0.0328	0.3623	-0.054	0.269	16.7924	14.6055	-16.9318
2	29.7768	0.254	-10.1339	10.0783	4.7571	6.0509	0.064	-0.2501	0.256	0.4229	0.3108	-0.4021	0.1926	0.2478	-0.3748	0.2114	-0.0088	-0.1424	0.0943	0.0178	0.2065	18.2263	14.9543	-0.2057
3	4.2164	0.1289	-0.6661	1.141	-0.4679	0.6018	0.2405	-0.3504	-0.0525	0.3419	-0.1412	0.0455	-0.1071	0.104	-0.0993	0.2138	0.011	-0.0022	0.1668	-0.0222	0.0664	-3.3412	4.9984	7.8164
4	1.7886	1.0794	1.0832	1.6139	0.1297	2.9157	0.0656	-0.1488	-0.103	0.1912	0.0089	0.1299	0.064	-0.3044	-0.0745	0.1085	-0.005	0.0207	0.2001	0.0386	0.1605	-18.4919	-7.2791	2.38
5	1.4442	-0.1623	0.3321	1.871	-1.0552	0.8881	-0.0863	0.0573	-0.0408	-0.0331	0.1134	0.0934	0.0906	-0.1087	-0.0271	0.1234	-0.0323	0.0032	0.1807	0.0057	0.1488	-16.2186	-9.7115	-9.1525
6	2.5444	-1.9872	-0.6593	4.0793	0.5175	0.1742	0.0983	-0.0191	-0.1326	0.219	-0.1228	0.0011	-0.0087	-0.0052	0.0244	0.1841	-0.0042	-0.0035	0.1654	0.0242	0.1283	-8.8366	-3.5442	1.5505
7	6.812	-7.5312	-4.8194	10.7742	-4.1796	40.3518	-1.3342	-0.1172	0.3442	1.6086	0.9163	-0.5202	1.1749	-2.3266	0.4179	0.4623	-0.0294	0.0994	0.3505	-0.0938	0.2448	-23.3723	1.2886	8.6793
8	4.8669	1.1199	-0.2482	1.4854	0.5519	0.318	-0.0808	-0.0901	-0.056	0.0692	-0.0014	0.0978	0.0428	0.0155	0.0822	0.1771	-0.0019	0.0087	0.1459	0.024	0.1303	-8.2954	-0.9034	-1.7948
9	4.7227	1.1171	1.6894	1.3941	0.5707	0.768	-0.1611	0.0194	0.0445	0.0152	0.075	0.0735	-0.0559	-0.0268	0.0861	0.1461	0.0052	-0.0098	0.1639	0.0071	0.1306	-4.9336	1.4385	-3.7718
10	12.8617	10.9808	4.8404	34.8576	7.517	2.2716	0.34	0.1848	-0.176	-1.4918	-0.4098	0.9535	-0.1122	-0.0127	0.0698	0.1988	0.1454	-0.0804	0.174	-0.0281	0.2422	-21.2997	7.9279	-6.0392
11	8.4942	-0.4276	2.2627	1.7081	-0.4095	0.6551	-0.0281	-0.1965	0.2606	0.1348	-0.0054	0.1355	-0.0264	-0.043	0.0336	0.1591	0.018	-0.0075	0.1689	-0.0371	0.1327	-8.9613	9.9339	2.0228
12	0.8475	-0.0897	0.6001	0.3397	0.0939	2.0612	-0.0282	-0.0563	0.1086	0.034	-0.007	-0.0151	0.1113	-0.1044	0.0352	0.1499	-0.003	-0.0189	0.1595	0.0043	0.1432	-0.3657	5.7731	-5.7565
13	1.2425	-0.5942	0.3974	0.7055	0.3442	0.9511	-0.011	0.0041	0.0869	-0.1046	-0.0002	0.0016	-0.0873	-0.1331	0.0112	0.1651	0.0004	-0.0316	0.1669	0.0328	0.1322	-5.6031	7.9369	-15.8733
14	6.0394	2.6407	-1.9191	3.3673	0.9349	2.0325	-0.1478	0.2718	-0.1943	-0.0055	-0.0241	0.0633	0.0844	-0.1929	0.1719	0.1751	-0.0034	-0.0334	0.1885	-0.0141	0.1152	-6.6563	-6.519	-22.1595
15	0.7549	-0.0265	0.0212	0.5602	0.2279	2.1201	-0.044	0.0043	0.1923	-0.0584	0.0464	0.0022	-0.2314	-0.0916	-0.0025	0.1626	0.0156	-0.0269	0.14	-0.006	0.174	-0.5458	12.4958	-6.825
16	4.3959	2.3373	2.1288	2.2661	2.0372	1.8528	0.0578	0.0375	0.5495	0.1263	-0.327	0.3128	0.1544	-0.2187	0.2691	0.1862	0.0384	-0.0312	0.283	-0.0137	0.1882	2.8409	-16.9595	-23.3066
17	0.7219	-0.8557	0.0401	3.841	-0.5894	3.6223	0.3017	0.027	-0.3139	-0.334	-0.2433	-0.0143	0.426	0.5103	-0.0583	0.2253	0.0708	-0.098	0.1862	-0.0059	0.2327	24.1107	-17.5427	-20.325
18	5.355	0.0513	1.3753	1.7723	0.3314	2.9844	0.1099	-0.1317	-0.0991	-0.0173	-0.155	-0.4214	0.3987	0.089	0.045	0.1098	-0.0011	-0.0232	0.1906	0.0595	0.1848	29.9517	-15.1869	-7.0378
19	2.8601	-2.6411	0.2555	5.3865	1.3746	4.0614	-0.3181	0.4803	0.9747	0.1968	0.0193	-0.6475	-0.2218	0.3042	0.2988	0.0455	-0.0719	-0.1106	0.166	0.1641	0.4792	28.3075	-0.1881	-7.079
20	12.001	-5.8249	3.9726	6.6274	-5.5221	4.7143	-0.0693	-0.1458	0.6235	0.1906	-0.2919	-0.4509	-0.1757	0.2957	0.3612	0.1167	0.0019	-0.087	0.1606	-0.0573	0.2369	26.9713	-5.9979	-0.8245
21	0.2706	-0.2011	0.4529	0.5786	0.3689	2.0135	0.0313	-0.0136	-0.0144	-0.0194	-0.0169	0.0309	0.1527	0.0282	-0.0144	0.154	0.0107	-0.0164	0.1584	0.0239	0.1579	18.9436	-12.8435	-6.4632
22	2.1338	-0.7424	-0.4359	0.9125	2.6689	9.7988	0.6368	0.4379	0.3292	-0.0343	0.087	-0.3135	0.5336	0.5638	-0.7238	0.2124	0.1622	0.0748	0.3078	-0.0095	0.3475	32.9808	-15.252	-18.7934
23	2.5306	0.0667	1.9568	1.1405	-0.0053	1.5223	0.0405	0.0031	0.0165	-0.1549	-0.0704	-0.1226	0.0191	0.038	0.0299	0.1768	-0.0095	-0.0017	0.1958	0.0204	0.1245	20.8237	-9.0226	-14.6764
24	9.4579	7.0407	1.6336	5.355	0.4412	5.8443	0.086	-0.3874	-0.0827	0.0711	-0.222	-0.0816	0.2594	-0.4726	0.136	0.2667	0.0589	-0.0152	0.1406	-0.0163	0.161	4.4053	-11.7034	-16.5403
25	6.0572	0.7334	2.1581	0.3787	-0.1658	1.7343	-0.0698	0.1191	0.001	-0.1349	-0.066	-0.0923	-0.054	0.2079	0.1358	0.2046	-0.0091	0.0041	0.149	0.0233	0.1741	20.4622	-5.4628	-16.1281
26	7.1475	3.2503	2.4513	2.05	1.2356	1.3775	0.0478	0.2187	-0.17	-0.1387	-0.1041	-0.0976	-0.0827	0.162	0.0564	0.1974	0.009	0.0222	0.1895	0.017	0.1054	21.1226	-8.4863	-25.4697
27	1.8078	0.8632	0.4435	3.1627	1.3096	0.5495	0.056	0.0994	-0.0238	-0.0947	0.0122	-0.1091	-0.0308	0.0179	-0.0682	0.1879	0.0014	-0.0163	0.1362	0.0055	0.1311	10.1524	-4.0167	-20.2914
28	1.4675	1.2525	0.5324	2.8522	0.7815	4.0907	-0.0838	0.2512	0.1631	-0.3804	0.076	-0.3215	-0.1331	0.3067	0.0077	0.1632	-0.0117	0.0585	0.1314	0.0316	0.1608	16.6036	5.5421	-21.908
29	0.7233	0.964	-0.8926	2.5893	-0.5949	1.373	-0.0589	0.0407	-0.0132	-0.0682	0.0597	-0.0648	0.0748	-0.045	-0.0009	0.1517	0.0016	-0.0105	0.1506	-0.0142	0.1742	8.2912	8.9718	-8.8096
30	0.3689	-0.3535	0.1942	1.0451	1.081	2.3833	0.064	0.0632	0.1341	-0.08	-0.0382	-0.1715	0.0249	0.0615	-0.0259	0.1665	0.0076	0.0044	0.142	0.002	0.1485	12.3884	2.8811	-17.1293

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 12
2	X-RAY DIFFRACTION	2	A	13 - 18
3	X-RAY DIFFRACTION	3	A	19 - 37
4	X-RAY DIFFRACTION	4	A	38 - 53
5	X-RAY DIFFRACTION	5	A	54 - 83
6	X-RAY DIFFRACTION	6	A	84 - 95
7	X-RAY DIFFRACTION	7	A	96 - 100
8	X-RAY DIFFRACTION	8	A	101 - 110
9	X-RAY DIFFRACTION	9	A	111 - 126
10	X-RAY DIFFRACTION	10	A	127 - 132
11	X-RAY DIFFRACTION	11	A	133 - 147
12	X-RAY DIFFRACTION	12	A	148 - 158
13	X-RAY DIFFRACTION	13	A	159 - 182
14	X-RAY DIFFRACTION	14	A	183 - 191
15	X-RAY DIFFRACTION	15	A	192 - 204
16	X-RAY DIFFRACTION	16	B	18 - 27
17	X-RAY DIFFRACTION	17	B	28 - 42
18	X-RAY DIFFRACTION	18	B	43 - 52
19	X-RAY DIFFRACTION	19	B	53 - 65
20	X-RAY DIFFRACTION	20	B	66 - 72
21	X-RAY DIFFRACTION	21	B	73 - 92
22	X-RAY DIFFRACTION	22	B	93 - 100
23	X-RAY DIFFRACTION	23	B	101 - 108
24	X-RAY DIFFRACTION	24	B	109 - 114
25	X-RAY DIFFRACTION	25	B	115 - 127
26	X-RAY DIFFRACTION	26	B	128 - 147
27	X-RAY DIFFRACTION	27	B	148 - 158
28	X-RAY DIFFRACTION	28	B	159 - 177
29	X-RAY DIFFRACTION	29	B	178 - 183
30	X-RAY DIFFRACTION	30	B	184 - 204

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-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

-
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