PDB-2y20: The mechanisms of HAMP-mediated signaling in transmembrane recept...

ID or keywords:

Entry

Database: PDB / ID: 2y20

Title

The mechanisms of HAMP-mediated signaling in transmembrane receptors - the A291I mutant

Components

UNCHARACTERIZED PROTEIN

Keywords

MEMBRANE PROTEIN / TRANSMEMBRANE SIGNALLING

Function / homology

Function and homology information

signal transduction / identical protein binding / membrane / metal ion binding
Similarity search - Function

Biological species

ARCHAEOGLOBUS FULGIDUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Zeth, K. / Ferris, H.U. / Hulko, M. / Lupas, A.N.

Citation

Journal: Structure / Year: 2011
Title: The Mechanisms of Hamp-Mediated Signaling in Transmembrane Receptors.
Authors: Ferris, H.U. / Dunin-Horkawicz, S. / Mondejar, L.G. / Hulko, M. / Hantke, K. / Martin, J. / Schultz, J.E. / Zeth, K. / Lupas, A.N. / Coles, M.

History

Deposition	Dec 12, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 20, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2011	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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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PDBx/mmCIF format	2y20.cif.gz	150.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2y20_validation.pdf.gz	468.2 KB	Display	wwPDB validaton report
Full document	2y20_full_validation.pdf.gz	472.9 KB	Display
Data in XML	2y20_validation.xml.gz	16.7 KB	Display
Data in CIF	2y20_validation.cif.gz	24.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y2/2y20 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y20	HTTPS FTP

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Related structure data

Related structure data	2l7hC 2l7iC 2y0qC 2y0tC 2y21C 3zrv 3zrw 3zrx C: citing same article (ref.)
Similar structure data	2y21-5 2y21-2 1o47-d 5c6c-2 1o4p-d 1o43-d 4eza-1 1o42-d 3tj2-2 1spr-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#158 - Feb 2013 Proton-Gated Urea Channel similarity (4) #190 - Oct 2015 Two-component Systems similarity (4)

Deposited unit

A: UNCHARACTERIZED PROTEIN

B: UNCHARACTERIZED PROTEIN

C: UNCHARACTERIZED PROTEIN

D: UNCHARACTERIZED PROTEIN

E: UNCHARACTERIZED PROTEIN

F: UNCHARACTERIZED PROTEIN

hetero molecules

39.4 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: UNCHARACTERIZED PROTEIN

B: UNCHARACTERIZED PROTEIN

hetero molecules

defined by author&software
13.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: UNCHARACTERIZED PROTEIN

D: UNCHARACTERIZED PROTEIN

hetero molecules

defined by author&software
13.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: UNCHARACTERIZED PROTEIN

F: UNCHARACTERIZED PROTEIN

hetero molecules

defined by author&software
13.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.490, 64.760, 93.110
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 280 - 328 / Label seq-ID: 7 - 55

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F

#1: Protein	UNCHARACTERIZED PROTEIN / AF1503 Mass: 6463.403 Da / Num. of mol.: 6 / Fragment: HAMP DOMAIN, RESIDUES 278-331 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: GENOMIC DNA / Plasmid: GST-FUSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28769
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.68 Å³/Da / Density % sol: 26.95 % / Description: NONE
Crystal grow	pH: 4.6 Details: 20 MM MOPS, 100 MM NACL, 0.1 M ZN ACETATE, 12% PEG 4000, PH 4.6.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→30 Å / Num. obs: 33647 / % possible obs: 99.1 % / Observed criterion σ(I): 2.7 / Redundancy: 6.2 % / R_merge(I) obs: 0.09 / Net I/σ(I): 22.7
Reflection shell	Resolution: 1.65→1.7 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 2.7 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.65→29.81 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.941 / SU B: 4.865 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.236	1775	5 %	RANDOM
R_work	0.189	-	-	-
obs	0.191	33647	98.3 %	-

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: 27.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0 Å²	0 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→29.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2576	0	9	200	2785

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	2714
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.087	1.986	3690
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.17	5	378
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.548	23.514	111
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.293	15	557
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.609	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.148	0.2	457
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	1959
X-RAY DIFFRACTION	r_gen_planes_other
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	1.263	1.5	1737
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.069	2	2847
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.363	3	977
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.444	4.5	818
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 340 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	medium positional	0.51	0.5
2	B	medium positional	0.46	0.5
3	C	medium positional	0.51	0.5
4	D	medium positional	0.8	0.5
5	E	medium positional	0.46	0.5
6	F	medium positional	0.42	0.5
1	A	medium thermal	2.34	2
2	B	medium thermal	2.09	2
3	C	medium thermal	2.91	2
4	D	medium thermal	2.08	2
5	E	medium thermal	2.44	2
6	F	medium thermal	2.48	2

LS refinement shell

Resolution: 1.65→1.69 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	152	-
R_work	0.243	2485	-
obs	-	-	99.43 %

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	2.7346	-0.5841	-0.6735	1.8859	0.1185	1.8081	-0.0017	-0.0137	-0.2375	-0.1396	-0.0447	0.2048	-0.0051	-0.3263	0.0464	0.0402	0.002	-0.004	0.069	-0.0087	0.0915	-19.851	4.812	-16.668
2	1.3144	0.652	-0.5944	1.9229	0.8367	6.503	-0.0952	-0.007	-0.2876	-0.0789	0.0285	-0.0406	0.3085	0.0555	0.0666	0.0619	0.019	0.0077	0.0217	-0.0025	0.0925	-12.192	-1.209	-18.68
3	3.3749	-1.3448	3.5876	5.3077	1.3059	5.5118	-0.1229	-0.3305	0.0013	-0.0199	0.1833	-0.041	-0.1278	-0.1583	-0.0604	0.0475	0.0501	0.0156	0.2626	-0.0328	0.0688	-6.75	6.346	-9.132
4	1.4474	0.9974	1.9127	1.6063	2.7744	6.7569	0.025	0.1924	0.0238	-0.0711	-0.037	-0.0017	-0.0835	-0.0332	0.0119	0.0625	0.0405	0.0036	0.0793	-0.0045	0.0595	-10.441	7.283	-29.3
5	3.687	0.8935	1.5435	1.6149	0.0089	4.3729	0.0296	0.2184	0.2461	0.0098	-0.0494	0.0654	-0.253	-0.1656	0.0197	0.0645	0.0358	-0.0165	0.0473	0.0083	0.067	-14.32	14.677	-23.047
6	11.8154	-1.3362	7.5	6.3859	6.3486	13.1205	0.1043	0.2219	0.2503	-0.2263	-0.2482	-0.014	-0.2029	-0.0646	0.1439	0.154	-0.0674	0.0278	0.0842	-0.0125	0.067	-11.063	21.519	-10.818
7	3.7737	-0.3229	4.6201	0.7719	-1.3383	6.9123	0.3078	0.5835	-0.0508	-0.1144	-0.2325	-0.0175	0.5647	0.917	-0.0752	0.1997	0.0858	-0.0364	0.2033	-0.0226	0.1193	13.708	-0.055	-7.171
8	3.4826	-1.1397	-0.1838	2.8959	1.2489	10.0203	0.0866	-0.0764	-0.1534	0.1478	-0.0389	0.0822	0.8505	-0.1167	-0.0478	0.1244	-0.0015	-0.0189	0.0435	-0.0257	0.0534	4.32	-1.023	-8.264
9	0.0522	-0.3133	-0.8331	2.0944	5.7609	16.0467	-0.017	0.0009	0.0074	0.3196	0.1115	-0.0334	1.068	0.4169	-0.0945	0.2436	0.144	-0.016	0.1047	-0.0364	0.0657	7.287	-2.815	-22.287
10	4.2775	-0.4476	2.0692	1.5275	0.3504	13.3955	-0.2008	0.3814	0.5479	0.0214	-0.0729	-0.072	-0.8341	0.0615	0.2737	0.0971	0.0189	-0.0452	0.0785	0.0214	0.1189	5.99	11.494	-14.695
11	1.5408	0.5695	4.4458	7.2611	-3.0504	16.9708	-0.4097	0.1714	0.3862	0.2946	-0.2778	-0.0289	-1.1553	0.6927	0.6875	0.2244	-0.0658	-0.2756	0.1319	0.0584	0.4433	14.374	12.92	-7.009
12	4.2769	-3.2392	-5.0151	5.5108	4.9557	19.8276	0.0118	0.3412	0.2848	-0.2384	0.1071	-0.3188	-0.7914	0.9187	-0.1189	0.0574	-0.1106	-0.0186	0.4302	0.1053	0.1782	17.199	8.867	-20.589
13	5.043	-3.1768	5.2721	19.6583	8.0155	12.7952	-0.2776	0.455	0.3917	-1.058	0.4079	-1.0773	-1.0705	0.9245	-0.1303	0.1891	-0.0629	0.0322	0.0731	0.0168	0.1788	24.286	7.468	2.964
14	4.4458	1.1374	-1.0806	1.2832	-1.4827	3.0773	-0.1056	0.2723	-0.0998	-0.2256	0.0043	0.0056	0.3446	0.0834	0.1012	0.1044	0.0268	-0.0056	0.0364	-0.0118	0.0668	24.787	-7.286	-0.817
15	25.4047	8.3951	8.4742	15.7316	-4.7593	15.3137	0.0382	1.3384	-2.8005	-0.7394	0.2505	-0.9308	2.0448	0.3682	-0.2887	0.5497	0.0398	0.1659	0.1116	-0.1859	0.4849	26.274	-21.177	-2.926
16	2.0739	3.0395	0.4418	7.7451	1.1692	2.9578	-0.0403	-0.3578	-0.1678	0.0303	-0.1096	-0.2772	0.2244	0.2939	0.15	0.078	0.0565	-0.0046	0.1618	0.0248	0.082	26.078	-8.652	12.572
17	3.3373	-4.3317	-2.5533	7.2621	0.0738	8.8959	-0.027	0.0532	0.1374	-0.0334	0.1105	-0.2414	-0.0567	-0.6129	-0.0835	0.0922	0.0808	0.0108	0.1438	-0.0007	0.1009	17.423	-5.19	12.504
18	1.7392	0.5415	3.4179	9.0404	-0.0364	6.8906	0.3548	-0.2444	-0.1653	-0.3777	0.0068	0.2694	0.8317	-0.5051	-0.3617	0.256	-0.0883	-0.0072	0.1045	0.0209	0.1322	15.038	-17.862	7.516

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	279 - 299
2	X-RAY DIFFRACTION	2	A	300 - 319
3	X-RAY DIFFRACTION	3	A	320 - 330
4	X-RAY DIFFRACTION	4	B	276 - 293
5	X-RAY DIFFRACTION	5	B	294 - 323
6	X-RAY DIFFRACTION	6	B	324 - 331
7	X-RAY DIFFRACTION	7	C	275 - 300
8	X-RAY DIFFRACTION	8	C	301 - 319
9	X-RAY DIFFRACTION	9	C	320 - 330
10	X-RAY DIFFRACTION	10	D	279 - 302
11	X-RAY DIFFRACTION	11	D	303 - 316
12	X-RAY DIFFRACTION	12	D	317 - 330
13	X-RAY DIFFRACTION	13	E	274 - 280
14	X-RAY DIFFRACTION	14	E	281 - 321
15	X-RAY DIFFRACTION	15	E	322 - 330
16	X-RAY DIFFRACTION	16	F	274 - 300
17	X-RAY DIFFRACTION	17	F	301 - 316
18	X-RAY DIFFRACTION	18	F	317 - 330

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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