PDB-2y0e: BceC and the final step of UGDs reaction

ID or keywords:

Entry

Database: PDB / ID: 2y0e

Title

BceC and the final step of UGDs reaction

Components

UDP-GLUCOSE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / CARBOHYDRATE SYNTHESIS / EXOPOLYSACCHARIDE / CYSTIC FIBROSIS

Function / homology

Function and homology information

UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / polysaccharide biosynthetic process / NAD binding
Similarity search - Function

Biological species

BURKHOLDERIA CEPACIA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Rocha, J. / Popescu, A.O. / Borges, P. / Mil-Homens, D. / Sa-Correia, I. / Fialho, A.M. / Frazao, C.

Citation

Journal: J.Bacteriol. / Year: 2011
Title: Structure of Burkholderia Cepacia Udp-Glucose Dehydrogenase (Ugd) Bcec and Role of Tyr10 in Final Hydrolysis of Ugd Thioester Intermediate.
Authors: Rocha, J. / Popescu, A.O. / Borges, P. / Mil-Homens, D. / Moreira, L.M. / Sa-Correia, I. / Fialho, A.M. / Frazao, C.

History

Deposition	Dec 2, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3	May 1, 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_initial_refinement_model / 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 / _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	2y0e.cif.gz	738.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2y0e.ent.gz	613.1 KB	Display	PDB format
PDBx/mmJSON format	2y0e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2y0e_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	2y0e_full_validation.pdf.gz	1.7 MB	Display
Data in XML	2y0e_validation.xml.gz	79.5 KB	Display
Data in CIF	2y0e_validation.cif.gz	116.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/2y0e ftp://data.pdbj.org/pub/pdb/validation_reports/y0/2y0e	HTTPS FTP

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Related structure data

Related structure data	2y0cC 2y0dC C: citing same article (ref.)
Similar structure data	2y0c-2 2y0c-1 2qg4-3 2o3j-2 4xrr-d 2qg4-2 5vr8-3 2o3j-3 5vr8-1 4edf-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: UDP-GLUCOSE DEHYDROGENASE

B: UDP-GLUCOSE DEHYDROGENASE

C: UDP-GLUCOSE DEHYDROGENASE

D: UDP-GLUCOSE DEHYDROGENASE

hetero molecules

214 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: UDP-GLUCOSE DEHYDROGENASE

D: UDP-GLUCOSE DEHYDROGENASE

hetero molecules

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

2

A: UDP-GLUCOSE DEHYDROGENASE

B: UDP-GLUCOSE DEHYDROGENASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.631, 108.933, 187.708
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 oper:

ID	Code	Matrix	Vector
1	given	(-0.01582, 0.9939, 0.1095), (0.9962, 0.006309, 0.08671), (0.08549, 0.1104, -0.9902)	72.3, -74.97, 35.23
2	given	(-0.06365, -0.9112, 0.4071), (-0.9108, -0.1137, -0.3968), (0.4079, -0.3961, -0.8227)	74.65, 83.16, 13.01
3	given	(-0.8691, -0.11, -0.4822), (-0.0641, -0.9417, 0.3304), (-0.4904, 0.3181, 0.8114)	74.65, 83.16, 13.01

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Protein , 1 types, 4 molecules ABCD

#1: Protein	UDP-GLUCOSE DEHYDROGENASE / BCEC Mass: 52295.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA CEPACIA (bacteria) / Strain: IST 408 / Plasmid: PBCEC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SURE / References: UniProt: C9E261, UDP-glucose 6-dehydrogenase

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Non-polymers , 5 types, 1401 molecules

#2: Chemical	ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID Mass: 580.285 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₂O₁₈P₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1373 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	CRYSTALLIZED BCEC CONTAINS ADDITIONAL N-TERMINAL TAG HHHHHHSG

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 49.5 % / Description: NONE
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: AT 293 K UPON VAPOR DIFFUSION OF SITTING DROPS OF 1 MICRO-LITER PROTEIN SOLUTION (5 MG/ML PROTEIN, 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT, 0.25 MM UDP-GLCA, AND 0.5 MM OXIDIZED NAD), ...Details: AT 293 K UPON VAPOR DIFFUSION OF SITTING DROPS OF 1 MICRO-LITER PROTEIN SOLUTION (5 MG/ML PROTEIN, 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT, 0.25 MM UDP-GLCA, AND 0.5 MM OXIDIZED NAD), AND 1 MICRO-LITER WELL SOLUTION (200 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE PH 4.5, 11 % (W/V) PEG 4K, AND 50 MM NAF), EQUILIBRATED AGAINST 500 MICRO-LITER PRECIPITATION SOLUTION IN THE WELL.

Crystal

Density Matthews: 2.39 Å³/Da / Density % sol: 49.5 % / Description: NONE

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: AT 293 K UPON VAPOR DIFFUSION OF SITTING DROPS OF 1 MICRO-LITER PROTEIN SOLUTION (5 MG/ML PROTEIN, 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT, 0.25 MM UDP-GLCA, AND 0.5 MM OXIDIZED NAD), ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9334 Å / Relative weight: 1
Reflection	Resolution: 1.75→47.56 Å / Num. obs: 197721 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / B_iso Wilson estimate: 18.31 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 6.7
Reflection shell	Resolution: 1.75→1.84 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PRELIMINARY (MAINLY POLY-ALA) MODEL OF SPHINGOMONAS ELODEA UGD (SEE REFERENCE 2 IN REMARK 1)

Resolution: 1.75→35.689 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 13.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1967	9969	5.04 %
R_work	0.1627	-	-
obs	0.1649	197642	98.19 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.484 Å² / k_sol: 0.376 e/Å³

Displacement parameters

B_iso mean: 24.4 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.75→35.689 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14051	0	270	1373	15694

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	14923
X-RAY DIFFRACTION	f_angle_d	1.398	20234
X-RAY DIFFRACTION	f_dihedral_angle_d	13.224	5615
X-RAY DIFFRACTION	f_chiral_restr	0.114	2240
X-RAY DIFFRACTION	f_plane_restr	0.006	2647

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 (%)
1.75-1.7699	0.2565	334	0.2565	6277	X-RAY DIFFRACTION	100
1.7699-1.7907	0.2338	330	0.2338	6277	X-RAY DIFFRACTION	100
1.7907-1.8126	0.2246	341	0.2246	6284	X-RAY DIFFRACTION	100
1.8126-1.8355	0.1971	335	0.1971	6304	X-RAY DIFFRACTION	100
1.8355-1.8596	0.2015	324	0.2015	6296	X-RAY DIFFRACTION	100
1.8596-1.8851	0.1791	319	0.1791	6292	X-RAY DIFFRACTION	99
1.8851-1.912	0.1679	339	0.1679	6292	X-RAY DIFFRACTION	100
1.912-1.9406	0.1611	367	0.1611	6253	X-RAY DIFFRACTION	100
1.9406-1.9709	0.1547	332	0.1547	6284	X-RAY DIFFRACTION	99
1.9709-2.0032	0.149	341	0.149	6292	X-RAY DIFFRACTION	99
2.0032-2.0378	0.152	330	0.152	6257	X-RAY DIFFRACTION	99
2.0378-2.0748	0.1586	305	0.1586	6276	X-RAY DIFFRACTION	99
2.0748-2.1147	0.19	340	0.19	6313	X-RAY DIFFRACTION	99
2.1147-2.1579	0.1778	334	0.1778	6247	X-RAY DIFFRACTION	99
2.1579-2.2048	0.152	328	0.152	6269	X-RAY DIFFRACTION	99
2.2048-2.2561	0.1499	337	0.1499	6259	X-RAY DIFFRACTION	99
2.2561-2.3125	0.1444	351	0.1444	6254	X-RAY DIFFRACTION	99
2.3125-2.375	0.1441	362	0.1441	6220	X-RAY DIFFRACTION	98
2.375-2.4449	0.1533	309	0.1533	6266	X-RAY DIFFRACTION	98
2.4449-2.5237	0.1525	331	0.1525	6257	X-RAY DIFFRACTION	98
2.5237-2.6139	0.1561	328	0.1561	6262	X-RAY DIFFRACTION	98
2.6139-2.7185	0.1635	311	0.1635	6231	X-RAY DIFFRACTION	97
2.7185-2.8422	0.1708	350	0.1708	6205	X-RAY DIFFRACTION	98
2.8422-2.992	0.1707	316	0.1707	6241	X-RAY DIFFRACTION	97
2.992-3.1793	0.1694	332	0.1694	6222	X-RAY DIFFRACTION	97
3.1793-3.4246	0.1614	278	0.1614	6274	X-RAY DIFFRACTION	97
3.4246-3.7689	0.1547	336	0.1547	6225	X-RAY DIFFRACTION	96
3.7689-4.3135	0.1455	359	0.1455	6162	X-RAY DIFFRACTION	96
4.3135-5.4315	0.1454	333	0.1454	6212	X-RAY DIFFRACTION	95
5.4315-35.6963	0.2041	335	0.2041	6158	X-RAY DIFFRACTION	91

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	0.6552	-0.4167	0.3806	0.572	0.0162	0.7737	-0.0319	0.0038	0.0392	-0.0494	0.0095	0.1907	-0.0442	0.0269	0	0.1537	-0.0052	-0.0138	0.1135	0.0115	0.1304	57.8503	10.0567	-7.4078
2	0.5325	-0.3029	0.3306	0.747	-0.3769	0.9419	0.0651	0.1091	-0.0111	-0.0868	-0.0566	0.0436	0.1531	0.1683	-0.0094	0.1148	0.0106	-0.0016	0.1302	-0.0079	0.0627	66.652	-1.8289	-7.6935
3	0.4126	-0.2551	-0.0173	0.3368	-0.1023	0.2033	0.0152	-0.0267	-0.0467	-0.0429	0.0083	0.0715	-0.0051	-0.0917	0.0363	0.0487	0.0066	-0.0069	0.0887	0.0011	0.0961	57.3564	-9.0035	17.6988
4	0.806	-0.2158	-0.3428	0.7559	0.5617	0.923	0.0193	-0.1194	0.1685	-0.0646	-0.0526	0.0596	-0.0754	-0.1271	-0.005	0.048	0.0455	0.0166	0.1365	-0.0202	0.1209	39.5185	6.499	24.4474
5	0.5738	-0.4493	0.2699	0.373	-0.2222	0.3134	-0.0328	-0.0615	-0.1409	0.2038	0.0565	-0.2093	-0.0297	0.0372	-0.0011	0.1336	0.0376	-0.0574	0.078	0.0092	0.114	81.918	-18.1553	48.2236
6	1.0821	-0.4924	0.8418	0.4734	-0.242	0.7193	-0.1392	-0.2036	-0.0122	0.2093	0.1647	-0.0027	-0.1614	-0.1767	-0.0078	0.1679	0.05	0.0239	0.1435	0.0039	0.0723	69.3605	-9.7731	47.8725
7	0.3101	-0.2214	0.2117	0.3754	-0.0337	0.2366	0.0041	-0.0338	-0.0565	0.0066	0.0284	0.0573	0.0247	-0.0487	0.0547	0.0543	0.0039	0.0042	0.0663	0.0085	0.0901	64.4953	-16.4769	21.681
8	0.4387	-0.177	-0.1013	1.0707	0.3692	0.8243	0.0602	-0.0274	0.0001	-0.0594	0.0502	-0.1369	0.0585	0.0674	0.215	0.0193	0.0109	-0.0114	0.0124	-0.0172	0.0482	80.7785	-33.3371	14.1557
9	0.5479	-0.1458	0.2369	0.3301	0.132	0.4083	-0.1945	-0.2538	0.6058	0.0007	-0.2103	0.4132	-0.0352	-0.2401	-0.0001	0.1509	0.0648	-0.0201	0.2633	-0.1398	0.5463	58.9509	31.9041	39.3134
10	1.5362	-0.2301	-0.1262	0.6023	-0.0477	0.361	-0.1657	-0.3658	0.1811	0.2421	-0.0024	0.2804	0.059	-0.1685	-0.042	0.1861	0.0471	0.0749	0.2106	-0.0761	0.1899	69.4754	24.7573	46.9349
11	0.3609	-0.1632	-0.0607	0.4863	-0.1301	0.2012	-0.0322	-0.0342	0.053	-0.0223	0.0169	0.0107	-0.1292	0.014	0.0034	0.098	0.0026	-0.0116	0.0488	-0.007	0.0654	87.1279	24.5319	25.6932
12	0.3051	-0.0911	-0.0289	1.5845	-0.3766	0.505	-0.0125	-0.01	0.0183	-0.437	0.0475	0.2108	0.0456	-0.0416	0.0783	0.2179	-0.0023	-0.0937	0.0425	-0.0009	0.0868	77.0147	36.1076	6.634
13	0.4873	-0.2981	-0.2605	0.6928	-0.2015	0.6903	-0.1706	-0.1101	-0.1221	0.0165	-0.0785	-0.3548	0.2851	0.0643	-0.0029	0.1492	0.0347	0.0463	0.1117	0.0494	0.2134	105.4839	-10.6157	13.2625
14	0.22	-0.2253	-0.2991	1.4238	0.2625	0.3356	-0.0195	0.0056	-0.026	-0.1028	-0.0303	-0.0866	-0.0102	-0.0523	-0.0428	0.0566	-0.0107	0.0317	0.0685	-0.0088	0.0718	98.8471	1.1854	4.9124
15	0.0778	-0.1987	-0.0528	0.4162	0.2378	0.2688	-0.0111	-0.0158	-0.0123	-0.019	0.0164	-0.0292	-0.0485	0.0535	-0.0219	0.0713	-0.0027	0.0014	0.078	-0.0054	0.0596	95.1862	17.0676	28.1067
16	0.7661	0.0113	0.6337	0.498	0.1507	1.6232	0.0299	-0.06	-0.1039	0.0566	0.0727	-0.0284	0.1509	0.1187	0.2221	0.0781	0.027	-0.0092	0.1132	0.0124	0.0658	105.9982	6.6252	47.7331

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID -1:95)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 96:205)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 206:303)
4	X-RAY DIFFRACTION	4	(CHAIN A AND (RESID 304:456 OR RESID 1501))
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID -1:95)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 96:205)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 206:303)
8	X-RAY DIFFRACTION	8	(CHAIN B AND (RESID 304:456 OR RESID 1501))
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID -1:95)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 96:205)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 206:303)
12	X-RAY DIFFRACTION	12	(CHAIN C AND (RESID 304:456 OR RESID 1501))
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID -1:95)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 96:205)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 206:303)
16	X-RAY DIFFRACTION	16	(CHAIN D AND (RESID 304:456 OR RESID 1501))

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 1401 molecules

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-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 1401 molecules

-
Details

-
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

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Yorodumi