PDB-5ih1: Macrolide 2'-phosphotransferase type II - complex with GDP and ph...

ID or keywords:

Entry

Database: PDB / ID: 5ih1

Title

Macrolide 2'-phosphotransferase type II - complex with GDP and phosphorylated josamycin

Components

Macrolide 2'-phosphotransferase II

Keywords

TRANSFERASE / macrolide phosphotransferase / kinase

Function / homology

Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / metal ion binding / Phosphorylated josamycin / GUANOSINE-5'-DIPHOSPHATE / Macrolide 2'-phosphotransferase II

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.31 Å

Authors

Berghuis, A.M. / Fong, D.H.

Funding support

Canada, 1items

Citation

Journal: Structure / Year: 2017
Title: Structural Basis for Kinase-Mediated Macrolide Antibiotic Resistance.
Authors: Fong, D.H. / Burk, D.L. / Blanchet, J. / Yan, A.Y. / Berghuis, A.M.

History

Deposition	Feb 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 3, 2017	Group: Database references
Revision 1.2	May 17, 2017	Group: Database references
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ih1.cif.gz	212.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ih1.ent.gz	171.8 KB	Display	PDB format
PDBx/mmJSON format	5ih1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ih1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5ih1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5ih1_validation.xml.gz	19.8 KB	Display
Data in CIF	5ih1_validation.cif.gz	30.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/5ih1 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/5ih1	HTTPS FTP

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Related structure data

Related structure data	5ighC 5igiC 5igjC 5igpC 5igrC 5igsC 5igtC 5iguC 5igvC 5igwC 5igyC 5igzC 5ih0C 5iwuC C: citing same article (ref.)
Similar structure data	5igj-d 5ih0-d 5oyd-1 5igw-d 5igs-d 5yy6-d 6szm-1 3dgv-4 5yw4-d 5z2x-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (2)

Deposited unit

A: Macrolide 2'-phosphotransferase II

hetero molecules

35.9 kDa, 1 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)	40.370, 80.870, 97.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	Macrolide 2'-phosphotransferase II / Macrolide 2'-phosphotransferase II protein MphB / Macrolide 2-phosphotransferase / mph(B) Mass: 34527.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mphB, pO103_99 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32553

#1: Protein

Macrolide 2'-phosphotransferase II / Macrolide 2'-phosphotransferase II protein MphB / Macrolide 2-phosphotransferase / mph(B)

Mass: 34527.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: mphB, pO103_99 / Plasmid: pET28a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32553

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Non-polymers , 5 types, 504 molecules

#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-6BQ / Phosphorylated josamycin / (2S,3S,4R,6S)-6-{[(2R,3S,4S,5R,6S)-6-{[(4R,5S,6S,7R,9R,10S,12E,16R)-4-(acetyloxy)-10-hydroxy-7-(2-hydroxyethyl)-5-methoxy-9,16-dimethyl-2-oxo-1-oxacyclohexadec-12-en-6-yl]oxy}-4-(dimethylamino)-2-methyl-5-(phosphonooxy)tetrahydro-2H-pyran-3-yl]oxy}-4-hydroxy-2,4-dimethyltetrahydro-2H-pyran-3-yl 3-methylbutanoate Mass: 912.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₂H₇₄NO₁₈P
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.26 Å³/Da / Density % sol: 45.6 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M calcium acetate, 0.1M Tris, 25-40% PEG 4000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 12, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.31→41.113 Å / Num. obs: 77829 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / R_merge(I) obs: 0.046 / Net I/σ(I): 21.66

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.31-1.34		0.661	3.1	1	100
1.34-1.38		0.512	4	1	100
1.38-1.42		0.412	4.93	1	100
1.42-1.46		0.317	6.4	1	100
1.46-1.51		0.24	8.4	1	100
1.51-1.57		0.188	10.5	1	100
1.57-1.62		0.146	13.5	1	100
1.62-1.69		0.118	16.46	1	100
1.69-1.77		0.096	19.72	1	100
1.77-1.85		0.078	23.75	1	100
1.85-1.95		0.061	29.98	1	100
1.95-2.07		0.051	34.96	1	100
2.07-2.21		0.044	39	1	100
2.21-2.39		0.041	42.21	1	100
2.39-2.62		0.038	44	1	100
2.62-2.93		0.036	46.36	1	100
2.93-3.38		0.033	48.83	1	100
3.38-4.14		0.032	50.23	1	100
4.14-5.86		0.035	50.28	1	100
	5.86	0.041	48.26	1	99.7

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Processing

Software

Name	Version	Classification
PHENIX	dev_1627	refinement
XSCALE		data scaling
PDB_EXTRACT	3.2	data extraction

Refinement

Resolution: 1.31→41.867 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1781	3892	5 %
R_work	0.1606	-	-
obs	0.1615	77827	99.98 %

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.31→41.867 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2401	0	92	500	2993

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2678
X-RAY DIFFRACTION	f_angle_d	1.357	3657
X-RAY DIFFRACTION	f_dihedral_angle_d	13.698	990
X-RAY DIFFRACTION	f_chiral_restr	0.069	395
X-RAY DIFFRACTION	f_plane_restr	0.006	463

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 (%)
1.3099-1.3259	0.2707	135	0.2547	2567	X-RAY DIFFRACTION	100
1.3259-1.3427	0.2414	140	0.2293	2648	X-RAY DIFFRACTION	100
1.3427-1.3604	0.2407	136	0.2176	2597	X-RAY DIFFRACTION	100
1.3604-1.379	0.2215	137	0.2072	2603	X-RAY DIFFRACTION	100
1.379-1.3987	0.2294	137	0.2117	2602	X-RAY DIFFRACTION	100
1.3987-1.4196	0.2289	137	0.197	2599	X-RAY DIFFRACTION	100
1.4196-1.4418	0.17	139	0.1905	2640	X-RAY DIFFRACTION	100
1.4418-1.4654	0.208	135	0.1771	2568	X-RAY DIFFRACTION	100
1.4654-1.4907	0.1938	138	0.1738	2627	X-RAY DIFFRACTION	100
1.4907-1.5178	0.1818	137	0.1697	2590	X-RAY DIFFRACTION	100
1.5178-1.547	0.1843	140	0.1755	2664	X-RAY DIFFRACTION	100
1.547-1.5785	0.1959	135	0.1666	2573	X-RAY DIFFRACTION	100
1.5785-1.6129	0.1964	140	0.1578	2645	X-RAY DIFFRACTION	100
1.6129-1.6504	0.1724	137	0.1556	2617	X-RAY DIFFRACTION	100
1.6504-1.6917	0.1556	139	0.1534	2636	X-RAY DIFFRACTION	100
1.6917-1.7374	0.1683	138	0.1582	2623	X-RAY DIFFRACTION	100
1.7374-1.7885	0.1885	138	0.1579	2629	X-RAY DIFFRACTION	100
1.7885-1.8462	0.1769	139	0.1659	2642	X-RAY DIFFRACTION	100
1.8462-1.9122	0.1896	138	0.1583	2607	X-RAY DIFFRACTION	100
1.9122-1.9888	0.1737	140	0.1531	2656	X-RAY DIFFRACTION	100
1.9888-2.0793	0.1897	140	0.151	2670	X-RAY DIFFRACTION	100
2.0793-2.1889	0.1816	138	0.1482	2620	X-RAY DIFFRACTION	100
2.1889-2.3261	0.1661	140	0.1484	2663	X-RAY DIFFRACTION	100
2.3261-2.5056	0.156	141	0.1441	2678	X-RAY DIFFRACTION	100
2.5056-2.7577	0.1623	140	0.1551	2662	X-RAY DIFFRACTION	100
2.7577-3.1567	0.1989	143	0.1632	2712	X-RAY DIFFRACTION	100
3.1567-3.9766	0.1409	143	0.1496	2728	X-RAY DIFFRACTION	100
3.9766-41.8882	0.1881	152	0.1634	2869	X-RAY DIFFRACTION	100

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	4.663	1.5393	0.4016	3.4732	0.663	3.2322	0.1038	-0.372	0.5215	0.5476	0.0504	-0.0009	-0.1645	0.1088	-0.1193	0.3877	0.0111	0.0437	0.3238	-0.053	0.2303	-10.9014	13.0361	52.4977
2	2.3954	-0.5434	-0.1093	2.351	-0.3166	1.821	-0.1988	0.0983	0.0743	0.4361	0.2022	-0.1881	-0.1054	0.4759	0.0299	0.2845	0.0053	-0.0062	0.3936	-0.0017	0.2074	-5.7915	7.1516	49.6292
3	2.0706	0.2914	-0.6977	1.6627	-0.988	2.7068	-0.0954	-0.3356	0.102	0.0356	-0.2035	-0.2145	0.0915	0.5209	0.2408	0.2231	0.0031	-0.0084	0.2923	-0.0015	0.154	-4.4764	8.933	44.2263
4	0.7726	0.423	-0.2854	2.8472	-1.7383	1.7864	-0.086	-0.1361	-0.1037	0.1301	-0.0547	-0.0551	0.2226	0.1833	0.0754	0.2241	0.0436	0.0376	0.2009	0.0313	0.1202	-7.8528	4.2138	44.4657
5	0.5188	-0.1972	0.2895	2.8318	1.3612	1.2337	-0.0481	0.0144	0.0277	-0.0549	-0.0146	0.1596	-0.1478	-0.0221	0.0536	0.1631	-0.0238	0.0342	0.1489	-0.0186	0.2008	-12.1653	9.9398	29.6771
6	1.4548	-0.6795	-0.5932	1.8268	0.3997	1.3728	-0.1998	-0.181	-0.1819	0.3389	0.0693	0.2922	0.1714	0.0588	0.1082	0.1506	0.013	0.0418	0.1328	0.0073	0.1387	-9.7321	2.8482	36.5927
7	4.8372	-1.5028	-1.8532	2.3491	0.3457	2.612	-0.1091	-1.0233	1.0133	0.3834	0.4408	-0.5161	-0.2106	0.6649	0.3361	0.2793	0.1535	-0.082	0.6187	-0.1708	0.206	10.3469	4.7412	38.1448
8	2.0896	-0.137	-0.633	7.5634	-1.0432	2.1937	-0.195	-0.9815	0.2876	-0.3264	0.1056	-0.8713	0.0821	0.4684	0.1535	0.2036	0.1219	-0.0352	0.5657	-0.0892	0.284	15.6833	0.0746	33.7546
9	3.3044	-0.39	0.2936	1.5554	0.0704	2.1534	-0.0418	-0.0176	-0.2349	0.094	0.0358	0.0213	0.2969	0.1478	0.0341	0.138	0.0202	0.0064	0.094	-0.0076	0.1247	1.7397	-6.6091	22.4511
10	6.4071	4.3029	0.7731	8.9103	0.1084	5.5129	-0.3585	0.3246	0.0173	0.08	-0.1946	-0.4369	-0.1014	0.1814	0.3269	0.155	-0.0075	-0.0135	0.2855	-0.0142	0.2985	-18.423	3.9869	18.1078
11	2.5511	0.7485	-0.2662	1.8769	-0.5129	1	-0.0095	0.3084	0.3656	-0.2323	0.0863	0.1566	-0.2992	-0.096	-0.0518	0.2065	0.0098	-0.0326	0.1531	0.0163	0.1321	-2.6678	12.924	9.7483
12	1.7055	-0.5188	0.3539	1.1752	0.421	1.1071	0.0093	0.1956	0.7032	-0.6046	0.0947	-0.612	-0.4269	0.218	-0.1005	0.314	-0.0711	0.0674	0.1993	0.0318	0.3702	12.2222	20.8859	9.7571
13	3.5294	1.6774	-0.2336	2.5043	-0.2343	1.1642	-0.0976	0.5138	-0.0894	-0.5602	0.0571	-0.1829	-0.1536	-0.1209	0.0125	0.2524	-0.017	0.0344	0.2229	-0.006	0.123	5.1219	5.7086	3.7691
14	1.2926	-0.275	-1.0605	1.2762	0.9164	1.4171	-0.1172	-0.1667	-0.0835	0.1302	0.1211	-0.0191	0.1441	0.2061	-0.0024	0.0922	0.0163	-0.0073	0.1113	0.0033	0.0853	2.18	1.2151	25.3063
15	2.1185	0.0062	-0.065	1.3997	0.0602	1.2231	-0.0642	0.0655	-0.1018	-0.1153	0.1511	-0.2278	0.0691	0.1676	-0.0709	0.1054	0.0079	0.0039	0.1148	-0.0368	0.1376	9.2077	-5.2144	16.2523
16	2.0519	0.3886	0.4548	3.6677	0.5249	1.223	-0.0099	0.0224	0.0543	-0.1354	0.0874	-0.3463	-0.1467	0.0905	-0.0683	0.1521	-0.0126	0.0199	0.1556	-0.0145	0.1613	10.2691	4.2066	11.4486
17	0.6519	-0.0641	-0.1976	2.0932	1.883	2.6985	-0.2564	-0.0256	0.0441	0.4681	0.0462	0.287	0.3172	-0.077	0.1401	0.3406	0.0139	-0.0296	0.1795	-0.0345	0.244	5.6631	21.1827	23.8058
18	2.9085	-0.5593	-1.0872	2.9457	1.2367	4.7301	-0.2575	-0.3742	0.4267	0.4249	0.1889	-0.836	-0.2516	0.2912	-0.0116	0.3649	0.0137	-0.1518	0.2485	-0.0513	0.4512	14.7353	22.5848	23.5942

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:14)
2	X-RAY DIFFRACTION	2	(chain A and resid 15:30)
3	X-RAY DIFFRACTION	3	(chain A and resid 31:41)
4	X-RAY DIFFRACTION	4	(chain A and resid 42:51)
5	X-RAY DIFFRACTION	5	(chain A and resid 52:74)
6	X-RAY DIFFRACTION	6	(chain A and resid 75:96)
7	X-RAY DIFFRACTION	7	(chain A and resid 97:107)
8	X-RAY DIFFRACTION	8	(chain A and resid 108:117)
9	X-RAY DIFFRACTION	9	(chain A and resid 118:140)
10	X-RAY DIFFRACTION	10	(chain A and resid 141:145)
11	X-RAY DIFFRACTION	11	(chain A and resid 146:163)
12	X-RAY DIFFRACTION	12	(chain A and resid 164:181)
13	X-RAY DIFFRACTION	13	(chain A and resid 182:193)
14	X-RAY DIFFRACTION	14	(chain A and resid 194:236)
15	X-RAY DIFFRACTION	15	(chain A and resid 237:258)
16	X-RAY DIFFRACTION	16	(chain A and resid 259:274)
17	X-RAY DIFFRACTION	17	(chain A and resid 275:286)
18	X-RAY DIFFRACTION	18	(chain A and resid 287:299)

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Protein , 1 types, 1 molecules A

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Non-polymers , 5 types, 504 molecules

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-Protein , 1 types, 1 molecules A

-Non-polymers , 5 types, 504 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+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

-
Structure viewers

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Viewer log

-
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

-
Downloads & links

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Download

-
Validation report

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Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 5 types, 504 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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