PDB-4hgz: Structure of the CcbJ Methyltransferase from Streptomyces caelestis

ID or keywords:

Entry

Database: PDB / ID: 4hgz

Title

Structure of the CcbJ Methyltransferase from Streptomyces caelestis

Components

CcbJ

Keywords

TRANSFERASE / S-adenosyl-L-methionine-dependent methyltransferase / Methyltransferase

Function / homology

Function and homology information

N-methyltransferase activity / methylation
Similarity search - Function

Biological species

Streptomyces caelestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Bauer, J.A. / Ondrovicova, G. / Kutejova, E. / Janata, J.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure and possible mechanism of the CcbJ methyltransferase from Streptomyces caelestis.
Authors: Bauer, J. / Ondrovicova, G. / Najmanova, L. / Pevala, V. / Kamenik, Z. / Kostan, J. / Janata, J. / Kutejova, E.

History

Deposition	Oct 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 16, 2014	Group: Database references
Revision 1.2	Feb 26, 2020	Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	4hgz.cif.gz	556.4 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hg/4hgz ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hgz	HTTPS FTP

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Related structure data

Related structure data	4hgyC 4hh4C C: citing same article (ref.)
Similar structure data	4hgy-d 4hh4-d 3mog-d 6tlk-d 1wzn-1 1exb-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
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: CcbJ

B: CcbJ

C: CcbJ

D: CcbJ

E: CcbJ

F: CcbJ

hetero molecules

181 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)	168.020, 244.550, 117.850
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-301- LI

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	CcbJ Mass: 30051.688 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: ccbJ / Plasmid: pET 28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E9JES0
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-LI / LITHIUM ION Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.36 Å³/Da / Density % sol: 63.36 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Na HEPES pH 7.5, 1.3 M Li2SO4.H2O, 10% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97549 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2009 / Details: Pd-coated toroidal mirror (Seso, France)
Radiation	Monochromator: 2 x channel-cut double-crystal silicon [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97549 Å / Relative weight: 1
Reflection	Resolution: 2.7→54.27 Å / Num. all: 66712 / Num. obs: 66712 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / B_iso Wilson estimate: 59.86 Å² / R_merge(I) obs: 0.071 / Net I/σ(I): 17.6
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.472 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9634 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→54.27 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.926 / SU B: 18.755 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.256 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22423	3353	5 %	RANDOM
R_work	0.18058	-	-	-
all	0.18279	63338	-	-
obs	0.18279	63338	99.82 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 63.183 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.44 Å²	-0 Å²	0 Å²
2-	-	2.42 Å²	0 Å²
3-	-	-	-0.98 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→54.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10736	0	58	136	10930

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	11015
X-RAY DIFFRACTION	r_angle_refined_deg	1.025	1.971	14967
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.554	5	1400
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.688	23.162	525
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.435	15	1676
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.819	15	102
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1654
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	8590
X-RAY DIFFRACTION	r_mcbond_it	4.517	1.5	6981
X-RAY DIFFRACTION	r_mcangle_it	6.501	2	11103
X-RAY DIFFRACTION	r_scbond_it	11.014	3	4034
X-RAY DIFFRACTION	r_scangle_it	14.277	4.5	3864

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1434	TIGHT POSITIONAL	0.28	0.05
1	2	B	1434	TIGHT POSITIONAL	0.46	0.05
1	3	C	1434	TIGHT POSITIONAL	0.3	0.05
1	4	D	1434	TIGHT POSITIONAL	0.25	0.05
1	5	E	1434	TIGHT POSITIONAL	0.25	0.05
1	6	F	1434	TIGHT POSITIONAL	0.25	0.05
1	1	A	1434	TIGHT THERMAL	1.7	0.5
1	2	B	1434	TIGHT THERMAL	1.98	0.5
1	3	C	1434	TIGHT THERMAL	2.11	0.5
1	4	D	1434	TIGHT THERMAL	1.73	0.5
1	5	E	1434	TIGHT THERMAL	2.01	0.5
1	6	F	1434	TIGHT THERMAL	1.6	0.5
2	1	A	7	TIGHT POSITIONAL	0.02	0.05
2	2	B	7	TIGHT POSITIONAL	0.06	0.05
2	3	D	7	TIGHT POSITIONAL	0.08	0.05
2	4	E	7	TIGHT POSITIONAL	0.04	0.05
2	5	F	7	TIGHT POSITIONAL	0.04	0.05
2	1	A	7	TIGHT THERMAL	2.23	0.5
2	2	B	7	TIGHT THERMAL	2.01	0.5
2	3	D	7	TIGHT THERMAL	0.95	0.5
2	4	E	7	TIGHT THERMAL	1.43	0.5
2	5	F	7	TIGHT THERMAL	1.5	0.5
3	1	A	876	TIGHT POSITIONAL	0.33	0.05
3	2	B	876	TIGHT POSITIONAL	0.38	0.05
3	3	F	876	TIGHT POSITIONAL	0.26	0.05
3	1	A	876	TIGHT THERMAL	1.26	0.5
3	2	B	876	TIGHT THERMAL	1.52	0.5
3	3	F	876	TIGHT THERMAL	1.06	0.5
4	1	A	8	TIGHT POSITIONAL	0.03	0.05
4	1	A	8	TIGHT THERMAL	0.58	0.5
5	1	C	85	TIGHT POSITIONAL	0.36	0.05
5	2	D	85	TIGHT POSITIONAL	0.41	0.05
5	3	E	85	TIGHT POSITIONAL	0.34	0.05
5	1	C	85	TIGHT THERMAL	2.79	0.5
5	2	D	85	TIGHT THERMAL	1.46	0.5
5	3	E	85	TIGHT THERMAL	2	0.5
6	1	A	18	TIGHT POSITIONAL	0.09	0.05
6	2	C	18	TIGHT POSITIONAL	0.08	0.05
6	3	E	18	TIGHT POSITIONAL	0.09	0.05
6	4	F	18	TIGHT POSITIONAL	0.09	0.05
6	1	A	18	TIGHT THERMAL	1.64	0.5
6	2	C	18	TIGHT THERMAL	2.84	0.5
6	3	E	18	TIGHT THERMAL	1.9	0.5
6	4	F	18	TIGHT THERMAL	1.31	0.5
7	1	B	18	TIGHT POSITIONAL	0.35	0.05
7	1	B	18	TIGHT THERMAL	1.3	0.5
8	1	A	22	TIGHT POSITIONAL	0.11	0.05
8	2	C	22	TIGHT POSITIONAL	0.14	0.05
8	3	D	22	TIGHT POSITIONAL	0.11	0.05
8	4	E	22	TIGHT POSITIONAL	0.14	0.05
8	5	F	22	TIGHT POSITIONAL	0.1	0.05
8	1	A	22	TIGHT THERMAL	1.54	0.5
8	2	C	22	TIGHT THERMAL	1.78	0.5
8	3	D	22	TIGHT THERMAL	1.16	0.5
8	4	E	22	TIGHT THERMAL	2.1	0.5
8	5	F	22	TIGHT THERMAL	1.2	0.5
9	1	A	32	TIGHT POSITIONAL	0.11	0.05
9	2	C	32	TIGHT POSITIONAL	0.17	0.05
9	3	D	32	TIGHT POSITIONAL	0.21	0.05
9	4	E	32	TIGHT POSITIONAL	0.13	0.05
9	5	F	32	TIGHT POSITIONAL	0.09	0.05
9	1	A	32	TIGHT THERMAL	1.84	0.5
9	2	C	32	TIGHT THERMAL	2.34	0.5
9	3	D	32	TIGHT THERMAL	1.43	0.5
9	4	E	32	TIGHT THERMAL	2.07	0.5
9	5	F	32	TIGHT THERMAL	1.04	0.5
10	1	A	18	TIGHT POSITIONAL	0.08	0.05
10	2	B	18	TIGHT POSITIONAL	0.1	0.05
10	3	D	18	TIGHT POSITIONAL	0.13	0.05
10	4	E	18	TIGHT POSITIONAL	0.06	0.05
10	5	F	18	TIGHT POSITIONAL	0.09	0.05
10	1	A	18	TIGHT THERMAL	1.1	0.5
10	2	B	18	TIGHT THERMAL	1.52	0.5
10	3	D	18	TIGHT THERMAL	1.16	0.5
10	4	E	18	TIGHT THERMAL	2.03	0.5
10	5	F	18	TIGHT THERMAL	0.76	0.5

LS refinement shell

Resolution: 2.7→2.77 Å / R_factor R_free error: 0.023 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.37	255	-
R_work	0.297	4587	-
obs	-	4842	99.96 %

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	4.3993	1.5175	-1.1473	7.156	-1.6291	2.5927	-0.0523	-0.5284	-0.1213	0.9155	-0.083	0.1657	-0.1912	-0.0672	0.1352	0.473	0.0388	-0.0233	0.1786	0.0915	0.3167	62.1113	-114.4092	80.2038
2	7.0164	-2.4779	0.1609	1.9601	0.835	1.1367	0.1427	-0.337	-0.0768	0.2057	0.0012	-0.0361	0.0866	-0.1648	-0.1439	0.2678	0.0044	0.0184	0.1566	0.1014	0.0916	59.1715	-90.6333	75.2333
3	3.9761	0.3083	-0.1688	5.0668	-0.5471	2.3217	-0.0149	0.1018	-0.4347	0.0147	-0.0586	-0.2029	0.3465	0.1829	0.0735	0.2837	0.0398	-0.0031	0.1315	0.0674	0.1798	74.5648	-108.5609	70.1541
4	10.993	-4.5091	-0.0841	5.0661	0.8489	4.5561	-0.2393	-2.0591	-0.4116	0.9204	0.2702	0.6261	0.0359	-1.1002	-0.0308	0.3197	0.0341	0.04	0.9994	0.1005	0.3074	22.4021	-76.343	56.5423
5	1.4565	1.3186	1.5699	2.998	2.8158	8.6911	0.0018	-0.1187	0.1618	0.0975	0.0831	0.3632	-0.0197	-0.1635	-0.0849	0.0825	0.0685	0.0128	0.2907	0.1317	0.2133	45.3418	-83.2371	66.2586
6	6.1808	-1.2899	0.5032	2.9523	0.6891	3.8793	0.0883	-0.2855	0.2335	-0.1049	0.0487	-0.0043	-0.2688	-0.4081	-0.1371	0.1037	0.0236	-0.0028	0.2123	0.129	0.1149	34.861	-80.2196	45.3377
7	4.3513	-1.3263	-0.0718	1.7237	0.2184	6.4273	-0.0356	-0.5968	-0.1702	0.1783	0.105	0.1386	0.4562	0.3495	-0.0694	0.1736	0.1837	-0.0244	0.4573	-0.1227	0.2625	68.2668	-56.8999	90.2754
8	2.3497	2.7159	-0.9662	7.4159	-3.3666	1.7944	-0.0574	-0.2793	0.1477	0.2262	0.0445	0.0832	-0.0088	-0.2563	0.013	0.2214	0.0366	0.0169	0.2939	-0.0416	0.118	57.0742	-72.6144	75.2242
9	3.81	-1.4703	0.0117	4.0497	1.0954	4.8627	-0.0305	-0.3451	0.3357	-0.1055	0.2076	-0.2482	-0.0696	0.5154	-0.1771	0.1196	0.0744	0.022	0.276	-0.1129	0.1793	71.9085	-53.8792	73.7819
10	2.5215	-0.5569	-0.0967	6.8173	0.3662	5.5465	-0.0049	0.9368	0.4973	-1.5733	-0.1514	-0.6039	-1.3627	-0.0409	0.1563	1.1506	0.2096	0.0162	0.568	0.1774	0.5619	64.2039	-46.8467	35.5961
11	2.0287	-0.9201	-0.9614	3.9416	2.9196	4.7103	-0.0981	-0.0673	0.1354	0.01	0.0602	0.0016	-0.1332	-0.018	0.0379	0.1536	0.0408	0.0512	0.0987	0.0567	0.1153	72.1786	-68.7774	44.2534
12	3.6324	-1.1539	0.2685	4.8409	0.7268	6.0595	0.0134	0.3135	0.6636	-0.693	-0.0235	0.3864	-0.7948	-0.671	0.0101	0.4597	0.1973	-0.0145	0.3235	0.0501	0.3144	60.4183	-49.1497	52.1271
13	3.1617	0.1215	-0.0269	7.4239	2.1631	4.2027	0.0135	0.7775	-0.1725	-1.2481	-0.0186	-0.6102	-0.0041	0.5534	0.0051	0.5671	-0.0096	0.035	0.3072	0.0482	0.4354	59.3024	-104.9743	26.4961
14	8.333	2.3072	0.2614	1.9932	-0.6029	1.1141	0.1268	0.0107	-0.0579	-0.0815	0.0914	0.0471	0.008	0.0201	-0.2182	0.1756	0.0028	0.0263	0.0742	0.0214	0.0651	66.7785	-85.1155	39.3617
15	3.4041	-0.6869	-0.9599	5.3104	0.4123	2.7354	0.0228	0.0494	-0.4084	-0.1683	0.0232	0.118	0.4277	-0.1901	-0.046	0.2078	-0.031	-0.0472	0.1072	0.1147	0.1886	47.9774	-100.1996	38.363
16	7.9786	1.3266	2.4261	5.1862	-1.9206	5.5567	0.0276	0.5951	0.1116	-0.6445	-0.2978	-1.4391	0.093	1.1828	0.2702	0.3462	-0.0099	0.0375	0.7686	0.1482	0.7928	104.1068	-84.0048	60.5047
17	0.9839	-0.603	0.4775	3.7904	-3.3926	6.0679	0.0264	-0.0278	0.0035	0.0119	-0.0133	-0.1916	0.1127	0.0202	-0.0131	0.1	0.0196	0.0293	0.1573	0.0192	0.1464	81.59	-83.4471	49.7115
18	5.0808	0.4556	0.0063	5.6092	-0.7921	3.8467	0.1413	-0.4636	0.0672	0.4295	-0.2108	-0.6993	-0.0341	0.6175	0.0695	0.2406	-0.0018	-0.0623	0.361	0.0794	0.2743	91.9008	-90.5356	70.3348

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 122
2	X-RAY DIFFRACTION	2	A	152 - 210
3	X-RAY DIFFRACTION	3	A	123 - 151
4	X-RAY DIFFRACTION	3	A	211 - 254
5	X-RAY DIFFRACTION	4	B	29 - 122
6	X-RAY DIFFRACTION	5	B	152 - 210
7	X-RAY DIFFRACTION	6	B	123 - 151
8	X-RAY DIFFRACTION	6	B	211 - 254
9	X-RAY DIFFRACTION	7	C	20 - 122
10	X-RAY DIFFRACTION	8	C	152 - 210
11	X-RAY DIFFRACTION	9	C	123 - 151
12	X-RAY DIFFRACTION	9	C	211 - 254
13	X-RAY DIFFRACTION	10	D	19 - 122
14	X-RAY DIFFRACTION	11	D	152 - 210
15	X-RAY DIFFRACTION	12	D	123 - 151
16	X-RAY DIFFRACTION	12	D	211 - 254
17	X-RAY DIFFRACTION	13	E	19 - 122
18	X-RAY DIFFRACTION	14	E	152 - 210
19	X-RAY DIFFRACTION	15	E	123 - 151
20	X-RAY DIFFRACTION	15	E	211 - 254
21	X-RAY DIFFRACTION	16	F	20 - 122
22	X-RAY DIFFRACTION	17	F	152 - 210
23	X-RAY DIFFRACTION	18	F	123 - 151
24	X-RAY DIFFRACTION	18	F	211 - 253

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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

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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