PDB-4eo2: Structure of the bacteriophage C1 tail knob protein, gp12

ID or keywords:

Entry

Database: PDB / ID: 4eo2

Title

Structure of the bacteriophage C1 tail knob protein, gp12

Components

Major tail protein

Keywords

STRUCTURAL PROTEIN / VIRAL PROTEIN

Function / homology

Distal tube protein, N-terminal / : / Caudoviral major tail protein N-terminus / Bacillus phage phi29, Tail knob protein gp9, C-terminal domain / identical protein binding / Major tail protein

Function and homology information

Biological species

Streptococcus phage C1 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.007 Å

Authors

Aksyuk, A.A. / Rossmann, M.G.

Citation

Journal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry.
Authors: Anastasia A Aksyuk / Valorie D Bowman / Bärbel Kaufmann / Christopher Fields / Thomas Klose / Heather A Holdaway / Vincent A Fischetti / Michael G Rossmann /

Abstract: The Podoviridae phage C1 was one of the earliest isolated bacteriophages and the first virus documented to be active against streptococci. The icosahedral and asymmetric reconstructions of the virus ...

History

Deposition	Apr 13, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 22, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2012	Group: Database references
Revision 1.2	Sep 12, 2012	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4eo2.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4eo2.ent.gz	999.1 KB	Display	PDB format
PDBx/mmJSON format	4eo2.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/eo/4eo2 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/4eo2	HTTPS FTP

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Related structure data

Related structure data	5445C 5446C 4ep0C C: citing same article (ref.)
Similar structure data	4ep0-2 4ep0-1 5fei-1 5w5f-d 5fb4-1 5fb5-1 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: Major tail protein

B: Major tail protein

C: Major tail protein

D: Major tail protein

E: Major tail protein

F: Major tail protein

401 kDa, 6 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)	205.614, 209.640, 102.975
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain 'A' and (resseq 3:49 or resseq 53:381 or resseq 462:573 ) and (not element H)
2	1	1	chain 'B' and (resseq 3:49 or resseq 53:381 or resseq 462:573 ) and (not element H)
3	1	1	chain 'C' and (resseq 3:49 or resseq 53:381 or resseq 462:573 ) and (not element H)
4	1	1	chain 'D' and (resseq 3:49 or resseq 53:381 or resseq 462:573 ) and (not element H)
5	1	1	chain 'E' and (resseq 3:49 or resseq 53:381 or resseq 462:573 ) and (not element H)
6	1	1	chain 'F' and (resseq 3:49 or resseq 53:381 or resseq 462:573 ) and (not element H)

#1: Protein	Major tail protein / tail knob protein / gp12 Mass: 66821.797 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus phage C1 (virus) / Gene: orf12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Y3F0

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.56 %
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 6 Details: 30% MPD, 0.1 M sodium citrate, pH 6.0, EVAPORATION, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1.00931, 1.00579, 1.00939

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2010

Radiation

Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.00931	1
2	1.00579	1
3	1.00939	1

Reflection

Resolution: 3.007→146.794 Å / Num. all: 88860 / Num. obs: 87794 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / R_merge(I) obs: 0.068 / R_sym value: 0.068 / Net I/σ(I): 27.44

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
3.007-3.11	5.8	0.425	3.74	0.425	1	91
3.11-3.23					1	97.5
3.23-3.38					1	99.7
3.38-3.56					1	100
3.56-3.78					1	100
3.78-4.07					1	100
4.07-4.48					1	100
4.48-5.13					1	99.8
5.13-6.46					1	100
6.46-50					1	99.5

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Processing

Software

Name	Classification
HKL-2000	data collection
SHELXCD	phasing
SHELXE	model building
RESOLVE	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Refinement

Method to determine structure:

MAD / Resolution: 3.007→50.002 Å / SU ML: 0.49 / σ(F): 1.89 / Phase error: 33.99 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2824	4387	5.02 %
R_work	0.2383	-	-
obs	0.2406	87392	98.04 %
all	-	88860	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 74.58 Å² / k_sol: 0.278 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	43.0455 Å²	-0 Å²	-0 Å²
2-	-	-30.4826 Å²	0 Å²
3-	-	-	-12.563 Å²

Refinement step

Cycle: LAST / Resolution: 3.007→50.002 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23688	0	0	0	23688

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	24180
X-RAY DIFFRACTION	f_angle_d	1.86	32784
X-RAY DIFFRACTION	f_dihedral_angle_d	18.762	8826
X-RAY DIFFRACTION	f_chiral_restr	0.099	3636
X-RAY DIFFRACTION	f_plane_restr	0.007	4260

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3948	X-RAY DIFFRACTION	POSITIONAL
1	2	B	3948	X-RAY DIFFRACTION	POSITIONAL	0.112
1	3	C	3948	X-RAY DIFFRACTION	POSITIONAL	0.105
1	4	D	3948	X-RAY DIFFRACTION	POSITIONAL	0.096
1	5	E	3948	X-RAY DIFFRACTION	POSITIONAL	0.102
1	6	F	3948	X-RAY DIFFRACTION	POSITIONAL	0.104

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 (%)
3.007-3.0415	0.5288	133	0.4368	2201	X-RAY DIFFRACTION	80
3.0415-3.0773	0.4943	123	0.3952	2508	X-RAY DIFFRACTION	90
3.0773-3.1148	0.4646	139	0.3644	2647	X-RAY DIFFRACTION	93
3.1148-3.1543	0.4146	118	0.3294	2659	X-RAY DIFFRACTION	96
3.1543-3.1957	0.4753	125	0.3361	2735	X-RAY DIFFRACTION	97
3.1957-3.2395	0.4263	141	0.3282	2749	X-RAY DIFFRACTION	98
3.2395-3.2858	0.3787	165	0.3222	2714	X-RAY DIFFRACTION	99
3.2858-3.3348	0.4034	176	0.3014	2766	X-RAY DIFFRACTION	99
3.3348-3.3869	0.4087	170	0.2879	2757	X-RAY DIFFRACTION	99
3.3869-3.4424	0.36	138	0.2921	2781	X-RAY DIFFRACTION	100
3.4424-3.5018	0.3833	141	0.3005	2782	X-RAY DIFFRACTION	100
3.5018-3.5654	0.3459	144	0.2826	2777	X-RAY DIFFRACTION	99
3.5654-3.634	0.3424	153	0.2879	2774	X-RAY DIFFRACTION	99
3.634-3.7082	0.3147	140	0.2752	2820	X-RAY DIFFRACTION	100
3.7082-3.7888	0.31	163	0.2652	2748	X-RAY DIFFRACTION	99
3.7888-3.8769	0.3059	123	0.258	2809	X-RAY DIFFRACTION	99
3.8769-3.9738	0.3329	160	0.2555	2805	X-RAY DIFFRACTION	99
3.9738-4.0812	0.2655	114	0.2336	2802	X-RAY DIFFRACTION	99
4.0812-4.2012	0.256	137	0.2276	2797	X-RAY DIFFRACTION	99
4.2012-4.3367	0.2874	158	0.2109	2785	X-RAY DIFFRACTION	99
4.3367-4.4916	0.2882	133	0.2091	2833	X-RAY DIFFRACTION	99
4.4916-4.6714	0.2691	148	0.2001	2814	X-RAY DIFFRACTION	99
4.6714-4.8838	0.2228	136	0.1946	2809	X-RAY DIFFRACTION	99
4.8838-5.141	0.2566	153	0.2038	2829	X-RAY DIFFRACTION	100
5.141-5.4628	0.2645	154	0.2088	2824	X-RAY DIFFRACTION	100
5.4628-5.8839	0.2361	168	0.213	2822	X-RAY DIFFRACTION	100
5.8839-6.4749	0.2324	167	0.2158	2861	X-RAY DIFFRACTION	100
6.4749-7.4093	0.2215	156	0.2072	2879	X-RAY DIFFRACTION	100
7.4093-9.325	0.2092	139	0.1845	2923	X-RAY DIFFRACTION	100
9.325-50.0084	0.2042	172	0.22	2995	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	0.0011	-0.0039	-0.0036	0.0054	-0.0062	0.0253	-0.0356	0.004	0.0494	0.0045	-0.0452	-0.0235	-0.0192	0.0016	-0.0078	0.5045	0.179	-0.0018	0.3521	0.1072	0.3759	78.3081	147.3525	34.6198
2	0.0354	0.0154	-0.0088	0.0086	-0.0055	0.0054	0.0508	-0.0232	0.1861	-0.0146	0.0396	-0.0622	-0.0484	-0.032	0.0967	0.4702	0.1162	-0.1932	0.3186	0.001	0.3223	75.1315	145.4555	37.0826
3	0.0944	0.0174	-0.083	0.0784	0.0361	0.1021	-0.0561	-0.0115	-0.044	0.0031	-0.0879	0.0641	0.0426	-0.115	-0.1071	0.2104	0.0551	-0.0428	0.2073	-0.0277	0.0938	101.1888	86.6944	82.3283
4	0.1211	-0.0127	0.0654	0.0347	0.0393	0.1427	0.0885	-0.0896	-0.0246	-0.0615	-0.0496	0.0198	-0.0297	-0.1456	0.152	0.017	0.0908	-0.0934	0.1781	-0.1628	-0.0215	87.5727	112.5266	63.309
5	0.0125	-0.0219	0.0138	0.0465	-0.0063	0.028	-0.0102	0.0195	-0.0076	0.0033	0.0127	-0.0105	-0.0104	-0.014	0.0279	0.1714	0.1927	-0.2763	0.1661	-0.1266	0.2842	62.5908	160.8624	62.2357
6	0.0009	-0.005	0.0024	0.0004	-0.0048	0.0049	-0.0005	0.0051	0.0184	0.0034	0.0339	0.014	-0.0162	-0.0128	0.022	0.2533	0.2286	-0.2053	0.2994	-0.0395	0.2668	63.4493	163.0163	55.0373
7	0.2071	-0.0651	-0.0873	0.0633	0.1592	0.2328	-0.243	-1.2447	-0.1311	0.3345	-0.3288	0.1959	0.0928	-0.1946	-1.2133	-0.3692	0.2488	-0.1837	-0.2262	-0.6266	-1.1556	75.6641	116.4984	91.6676
8	0.0168	0.0019	-0.0089	0.0009	-0.0005	0.0075	0.0172	-0.0149	-0.0053	-0.0028	0.0187	0.0072	-0.0206	-0.0005	0.0348	0.6384	0.1623	-0.3757	0.5311	-0.3334	0.6434	29.8316	152.6116	69.9236
9	0.0286	-0.0074	0.0142	0.0086	-0.0034	0.0096	0.0063	-0.0284	-0.0568	-0.0099	-0.0583	0.0785	0.0235	-0.0743	0	0.7048	0.1058	-0.4503	0.671	-0.2593	1.0242	31.5451	149.2521	67.5744
10	0.0057	0.0076	0.0147	0.1489	0.0182	0.0177	0.0707	-0.3627	-0.1953	0.1783	-0.1073	0.1653	0.1943	-0.2248	-0.0724	0.5018	-0.2025	0.0871	0.9839	0.1222	0.4935	54.9262	89.694	111.3739
11	0.2343	0.238	0.2462	0.2564	0.1692	0.4149	-0.1531	-0.3126	0.2083	-0.0686	-0.333	0.3857	-0.061	-0.2501	-0.4397	0.2626	0.1069	-0.0755	0.7146	-0.1917	0.418	45.1868	114.6327	89.6634
12	0.0083	-0.0054	0.0046	0.0069	0.002	0.0064	0.0619	0.0094	-0.0652	0.0274	0.0524	-0.0251	-0.0079	-0.0152	0.0001	0.8188	0.2868	-0.2292	0.4629	-0.1028	0.8699	11.6903	133.0656	50.0404
13	0.2026	-0.0012	-0.1226	0.0306	0.0226	0.0776	-0.0522	-0.1971	-0.0582	-0.0473	-0.1807	0.1553	0.0127	-0.0763	-0.0734	0.7099	-0.0453	-0.3314	0.6029	-0.1739	1.0132	27.1372	108.5664	62.6967
14	0.0151	0.0167	-0.0016	0.0192	0.0024	0.0088	0.0825	-0.0071	0.0308	-0.021	0.0117	0.0625	0.0046	-0.0564	0.0001	0.8363	-0.2837	-0.0628	0.8031	0.2142	0.8129	48.4337	57.7987	100.3589
15	0.2916	0.0665	-0.0589	0.1327	0.0489	0.3705	0.0296	-0.2752	-0.074	0.0241	-0.3326	0.2471	-0.0565	-0.2403	-0.5174	0.4306	-0.1828	-0.2864	0.4131	0.0056	0.8745	33.3461	91.0275	74.904
16	0.0041	0.0017	0.0075	0.0031	-0.0002	0.0087	0.0943	0.0238	-0.0014	0.0434	0.0075	-0.0224	0.0304	0.0506	0	0.9096	0.1217	-0.3877	0.6152	-0.0757	0.888	24.9023	118.8866	23.2584
17	0.0134	0.0172	0.017	0.0187	0.0194	0.0233	-0.0179	-0.0119	-0.0529	0.0358	0.0019	-0.0582	-0.0121	0.0632	0	0.8795	0.2114	-0.4116	0.6908	-0.05	0.8396	34.8654	116.2121	24.7069
18	0.0674	-0.0131	-0.0455	0.0173	0.0501	0.148	-0.0022	-0.1249	-0.1371	-0.0018	-0.1426	0.1044	0.0645	-0.0996	-0.1742	0.5937	-0.1778	-0.3482	0.3647	0.0537	0.7943	57.0996	64.4805	63.67
19	0.2886	0.226	0.0504	0.276	0.128	0.0943	-0.1698	0.1541	-0.2591	-0.1329	-0.134	0.1822	0.0009	-0.0976	-0.7147	0.7356	-0.284	-0.6933	0.0052	-0.181	0.8169	50.1723	77.4613	54.5097
20	0.0007	-0.0153	0.0027	0.0646	0.0053	0.0699	0.0186	0.0479	0.0315	-0.0201	-0.1059	0.0782	-0.0378	-0.017	-0.0474	0.6646	0.383	-0.252	0.5943	-0.2179	0.2513	58.9502	126.4059	12.9866
21	0.0462	-0.0227	-0.023	0.0333	-0.0101	0.0733	0.0256	0.1061	0.048	-0.0235	-0.1007	0.0693	-0.0956	-0.1453	0.0172	0.5286	0.2091	-0.1284	0.4646	-0.1275	0.2182	67.3791	117.3844	30.2888
22	0.0389	0.024	-0.0263	0.0385	0.0044	0.0544	0.02	0.0218	-0.0956	-0.1759	-0.0863	0.0214	-0.0154	-0.007	-0.0323	0.557	0.0477	-0.2301	0.1746	-0.0421	0.5593	90.1836	59.1831	66.3759
23	0.0743	-0.0401	0.0566	0.1668	0.0941	0.0427	0.1032	0.1044	-0.3739	-0.2939	-0.0575	0.1575	0.0156	0.0041	0.0021	0.5242	0.1682	-0.257	-0.1118	-0.4325	-0.0731	75.1191	94.0083	45.0428

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:60)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 61:135)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 136:276)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 277:573)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 3:60)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 61:97)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 98:573)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 3:60)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 61:135)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 136:285)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 286:573)
12	X-RAY DIFFRACTION	12	chain 'D' and (resseq 3:88)
13	X-RAY DIFFRACTION	13	chain 'D' and (resseq 89:177)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq 178:243)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 244:573)
16	X-RAY DIFFRACTION	16	chain 'E' and (resseq 3:73)
17	X-RAY DIFFRACTION	17	chain 'E' and (resseq 74:135)
18	X-RAY DIFFRACTION	18	chain 'E' and (resseq 136:215)
19	X-RAY DIFFRACTION	19	chain 'E' and (resseq 216:573)
20	X-RAY DIFFRACTION	20	chain 'F' and (resseq 3:88)
21	X-RAY DIFFRACTION	21	chain 'F' and (resseq 89:158)
22	X-RAY DIFFRACTION	22	chain 'F' and (resseq 159:276)
23	X-RAY DIFFRACTION	23	chain 'F' and (resseq 277:573)

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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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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