PDB-4dmz: PelD 156-455 from Pseudomonas aeruginosa PA14, apo form

ID or keywords:

Entry

Database: PDB / ID: 4dmz

Title

PelD 156-455 from Pseudomonas aeruginosa PA14, apo form

Components

Putative uncharacterized protein pelD

Keywords

Nucleotide-binding Protein / GAF domain / GGDEF domain / c-di-GMP receptor / Inner membrane / Gram negative bacteria

Function / homology

Function and homology information

membrane => GO:0016020 / nucleotide binding / membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.102 Å

Authors

Whitney, J.C. / Colvin, K.M. / Marmont, L.S. / Robinson, H. / Parsek, M.R. / Howell, P.L.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Structure of the Cytoplasmic Region of PelD, a Degenerate Diguanylate Cyclase Receptor That Regulates Exopolysaccharide Production in Pseudomonas aeruginosa.
Authors: Whitney, J.C. / Colvin, K.M. / Marmont, L.S. / Robinson, H. / Parsek, M.R. / Howell, P.L.

History

Deposition	Feb 8, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 23, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 30, 2012	Group: Database references
Revision 1.2	Jul 25, 2012	Group: Database references
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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site 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_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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4dmz.cif.gz	233.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4dmz.ent.gz	188.7 KB	Display	PDB format
PDBx/mmJSON format	4dmz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4dmz_validation.pdf.gz	465.4 KB	Display	wwPDB validaton report
Full document	4dmz_full_validation.pdf.gz	471.3 KB	Display
Data in XML	4dmz_validation.xml.gz	22.9 KB	Display
Data in CIF	4dmz_validation.cif.gz	31.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dm/4dmz ftp://data.pdbj.org/pub/pdb/validation_reports/dm/4dmz	HTTPS FTP

-
Related structure data

Related structure data	4dn0C C: citing same article (ref.)
Similar structure data	6hbc-d 1kz7-d 2wtf-d 2ffh-10 5oaw-d 4y7k-d 6ptu-d 5yoq-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (2) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2)

Deposited unit

A: Putative uncharacterized protein pelD

B: Putative uncharacterized protein pelD

hetero molecules

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

1

A: Putative uncharacterized protein pelD

B: Putative uncharacterized protein pelD

hetero molecules

A: Putative uncharacterized protein pelD

B: Putative uncharacterized protein pelD

hetero molecules

defined by author&software
146 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.511, 113.346, 61.846
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-608- HOH

#1: Protein	Putative uncharacterized protein pelD Mass: 36059.996 Da / Num. of mol.: 2 / Fragment: Soluble fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: pelD, PA14_24510 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02PM6, UniProt: A0A0H2ZD98*PLUS
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.81 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 11.5% PEG 8000, 0.1M Tris-HCl, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2011
Radiation	Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 36951 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.102→47.728 Å / SU ML: 0.67 / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2378	2000	5.41 %	Random
R_work	0.1956	-	-	-
obs	0.1979	36951	99.92 %	-
all	-	36980	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 54.444 Å² / k_sol: 0.336 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.5518 Å²	-0 Å²	0 Å²
2-	-	-8.0278 Å²	-0 Å²
3-	-	-	2.476 Å²

Refinement step

Cycle: LAST / Resolution: 2.102→47.728 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4175	0	40	129	4344

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4271
X-RAY DIFFRACTION	f_angle_d	0.993	5796
X-RAY DIFFRACTION	f_dihedral_angle_d	13.123	1560
X-RAY DIFFRACTION	f_chiral_restr	0.061	699
X-RAY DIFFRACTION	f_plane_restr	0.003	759

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 (%)
2.102-2.1544	0.2995	141	0.2463	2476	X-RAY DIFFRACTION	99
2.1544-2.2127	0.3228	141	0.2275	2458	X-RAY DIFFRACTION	100
2.2127-2.2778	0.281	139	0.213	2422	X-RAY DIFFRACTION	100
2.2778-2.3513	0.2739	141	0.2187	2469	X-RAY DIFFRACTION	100
2.3513-2.4353	0.2628	141	0.2121	2459	X-RAY DIFFRACTION	100
2.4353-2.5328	0.2972	143	0.2162	2492	X-RAY DIFFRACTION	100
2.5328-2.6481	0.2878	140	0.2163	2452	X-RAY DIFFRACTION	100
2.6481-2.7877	0.2585	142	0.2192	2487	X-RAY DIFFRACTION	100
2.7877-2.9623	0.3406	143	0.2269	2492	X-RAY DIFFRACTION	100
2.9623-3.191	0.3016	141	0.2136	2484	X-RAY DIFFRACTION	100
3.191-3.5121	0.2381	144	0.199	2507	X-RAY DIFFRACTION	100
3.5121-4.02	0.2254	145	0.1717	2531	X-RAY DIFFRACTION	100
4.02-5.0639	0.1682	145	0.1509	2540	X-RAY DIFFRACTION	100
5.0639-47.74	0.2131	154	0.2083	2682	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	3.189	-2.8079	-2.5037	2.8346	3.1801	5.2178	-0.334	-0.2905	0.5894	-0.4227	0.9562	-1.0699	-0.3272	0.3315	-0.5617	0.3647	-0.0487	0.0018	0.3412	-0.0895	0.4042	25.9518	-11.279	-35.4279
2	7.4469	1.1776	-0.4008	3.0997	-0.5009	7.8083	0.1247	-0.201	1.1688	-0.0217	0.2155	0.3127	-0.8353	-0.7741	-0.2223	0.1966	0.0779	0.0307	0.4379	-0.12	0.4026	14.2312	-8.7601	-30.6902
3	1.3007	-1.3961	-2.4364	2.6156	1.618	5.723	0.232	-0.854	0.2913	0.2906	-0.3052	0.5624	-0.1798	-1.2319	0.1569	0.3805	-0.0581	0.1642	0.9603	-0.2724	0.5121	7.9651	-14.2426	-21.2562
4	3.075	-0.3214	1.91	4.3575	0.1219	1.2199	-0.3115	-1.0969	-0.185	1.1058	-0.3867	0.4475	0.3811	-1.3421	0.5318	0.3727	-0.1322	0.1526	1.3087	-0.2335	0.6335	1.6926	-18.3018	-22.8277
5	3.7171	0.1335	-1.8823	5.9837	1.266	6.4289	0.3195	-0.9997	-0.0244	0.8677	-0.2911	0.2807	0.9804	-0.3394	-0.0241	0.4055	-0.1583	0.0703	0.6022	-0.045	0.2949	12.6166	-23.4769	-20.5816
6	9.5298	5.1249	2.9057	3.1229	3.167	7.3948	0.0456	0.0138	-0.0389	0.4367	-0.0272	-0.4249	0.6361	0.0623	-0.0025	0.3356	-0.0468	0.0171	0.3172	-0.0259	0.2461	21.0412	-19.3476	-25.9435
7	4.3427	3.864	1.9219	4.0835	3.1352	4.1556	0.0375	-0.396	0.6399	-0.056	-0.2011	0.5645	0.0462	-0.1387	0.1654	0.304	-0.0101	-0.0031	0.276	-0.019	0.3718	32.7988	-14.651	-20.0557
8	7.9717	5.9856	-1.3426	9.1189	-2.7704	5.2616	-0.1584	0.3167	0.4703	-0.2901	-0.0821	-0.0886	0.2093	0.6512	0.1582	0.2422	0.0663	0.0672	0.284	0.0199	0.3091	49.2285	-8.8316	-29.4172
9	5.6914	5.4364	1.814	5.2854	2.5684	6.3412	0.1728	0.4994	0.0011	-0.0871	0.252	-0.1591	0.3864	0.3169	-0.3236	0.261	0.0414	-0.0363	0.2034	0.0093	0.273	43.6623	-11.2865	-26.1675
10	7.9093	4.0368	1.6575	4.7917	2.4419	4.4712	0.0594	1.5907	0.3255	-0.417	0.3145	-0.2224	-0.0885	-0.5903	-0.2799	0.4846	0.135	0.0545	0.7713	0.0865	0.2943	48.2105	-10.0013	-39.8587
11	4.8157	5.1401	-3.374	5.6755	-4.3703	6.0207	-0.6685	0.734	-0.7576	-1.161	0.4288	-0.6934	1.023	0.6799	0.4081	0.4901	0.0884	0.0741	0.5349	-0.0163	0.4775	52.9854	-15.1068	-31.6173
12	3.0307	1.8455	1.6164	6.5742	-1.5441	2.8225	-0.0904	-0.5896	-0.4588	0.4932	-0.1906	0.5723	0.6558	-0.1925	0.2105	0.4566	0.0201	0.0379	0.337	-0.0291	0.3818	44.4084	-19.2321	-15.5025
13	3.066	-3.6513	-2.7095	5.9732	2.3503	9.0946	0.1031	-1.0859	0.9081	-0.0242	-0.033	0.1184	-0.6773	0.6381	0.0471	0.3356	-0.1072	-0.0367	0.3784	0.0096	0.315	23.0478	-9.6815	-41.6004
14	6.2366	1.4852	-0.9467	2.6388	-1.3136	7.5853	0.243	0.1411	0.3007	-0.348	0.1788	-0.5541	0.3873	1.2787	-0.2863	0.376	0.0382	0.057	0.5195	-0.1025	0.3807	28.4736	-20.3066	-45.9102
15	5.3446	0.2748	-2.7148	5.0341	-0.3292	5.0706	0.2371	0.1884	0.0648	-0.8962	0.0304	-0.3272	0.0556	0.5938	-0.2918	0.4098	-0.021	0.015	0.3184	-0.1042	0.2443	24.1092	-28.6242	-54.4169
16	3.9454	2.6835	5.01	4.9426	3.7182	6.4055	0.1437	0.6305	-0.8364	-0.6348	0.2297	-0.3075	1.4382	0.3112	-0.366	0.5704	-0.0152	0.0364	0.3535	-0.0732	0.3377	21.3968	-35.752	-51.9312
17	6.0847	1.313	-2.0375	5.5986	-0.0047	3.8273	-0.1058	0.552	-0.037	-0.6695	0.1632	0.2763	-0.1348	-0.1005	-0.0494	0.3608	-0.0779	-0.0221	0.288	-0.0267	0.2129	14.1764	-26.2406	-54.8849
18	8.3579	3.2785	-0.6579	2.9732	-0.8704	6.7924	-0.0181	0.7899	0.1127	-0.1565	0.2093	-0.0546	-0.0887	0.1609	-0.2048	0.3496	-0.0495	0.0041	0.2446	-0.0144	0.2765	17.9458	-15.7062	-51.0913
19	3.9229	0.7133	-3.9611	8.9348	-3.1134	4.6742	0.2687	0.6187	-0.3481	-0.6488	0.2645	0.0297	0.2835	-0.5335	-0.5051	0.4656	-0.0366	-0.024	0.4178	0.014	0.4074	16.565	-5.0231	-56.8538
20	3.0072	2.1502	-0.7802	6.6697	-1.553	4.088	0.492	-0.0384	0.0272	1.1531	-0.5287	-0.6348	-1.0538	0.2664	0.0774	0.615	-0.0326	-0.0254	0.4169	0.1233	0.3754	16.2157	12.5047	-48.6542
21	1.372	-0.221	-0.1556	2.8945	-1.542	6.5664	0.2931	0.0798	-0.0722	1.1129	-0.3037	0.0358	-0.8071	0.3881	0.0453	0.4544	-0.0745	-0.0081	0.3758	0.1341	0.3374	16.9814	7.529	-51.3292
22	1.2735	-0.0497	-0.1934	0.8002	-0.6851	0.6227	0.0049	-0.136	0.5075	0.0784	-0.1201	-0.2856	-0.8596	0.3555	-1.0503	2.1164	-0.4652	0.3947	0.1016	0.1709	0.347	14.7945	14.0387	-37.5769
23	1.8095	2.5854	1.5615	7.9542	5.6128	4.3846	0.3187	-0.1025	0.5853	0.7296	0.0386	1.2402	-1.2669	-0.714	-0.4181	0.8125	0.1239	0.2029	0.3748	0.2175	0.5903	9.0638	12.5871	-48.8014
24	8.6083	4.2089	-1.1924	2.7226	-0.5467	4.5221	-0.4063	1.065	-0.5698	-1.7982	0.5606	0.7908	0.4936	-1.3256	-0.119	0.6832	-0.0159	-0.0495	0.5742	0.0583	0.6111	9.6952	3.9787	-61.8527

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 156:173)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 174:195)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 196:217)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 218:230)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 231:289)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 290:308)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 318:338)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 339:365)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 366:396)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 397:411)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 412:429)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 430:455)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 156:173)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 174:195)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 196:217)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 218:230)
17	X-RAY DIFFRACTION	17	(CHAIN B AND RESID 231:289)
18	X-RAY DIFFRACTION	18	(CHAIN B AND RESID 290:310)
19	X-RAY DIFFRACTION	19	(CHAIN B AND RESID 319:338)
20	X-RAY DIFFRACTION	20	(CHAIN B AND RESID 339:365)
21	X-RAY DIFFRACTION	21	(CHAIN B AND RESID 366:396)
22	X-RAY DIFFRACTION	22	(CHAIN B AND RESID 397:415)
23	X-RAY DIFFRACTION	23	(CHAIN B AND RESID 416:429)
24	X-RAY DIFFRACTION	24	(CHAIN B AND RESID 430:455)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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