PDB-2y0c: BceC mutation Y10S

ID or keywords:

Entry

Database: PDB / ID: 2y0c

Title

BceC mutation Y10S

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	Dec 20, 2023	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	2y0c.cif.gz	739.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2y0c.ent.gz	613.1 KB	Display	PDB format
PDBx/mmJSON format	2y0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/2y0c ftp://data.pdbj.org/pub/pdb/validation_reports/y0/2y0c	HTTPS FTP

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Related structure data

Related structure data	2y0dC 2y0eSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2qg4-3 2y0e-1 2y0e-2 2qg4-2 4xrr-d 4xr9-d 2o3j-2 5vr8-3 2o3j-3 5vr8-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

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)

2

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)

Unit cell

Length a, b, c (Å)	97.358, 108.620, 187.464
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	(-0.01687, 0.9937, 0.1107), (0.9963, 0.007397, 0.08547), (0.08412, 0.1117, -0.99)	72.15, -74.69, 35.4
2	given	(-0.06221, -0.9112, 0.4073), (-0.9107, -0.1151, -0.3967), (0.4084, -0.3956, -0.8227)	74.28, 83.04, 13.07
3	given	(-0.869, -0.107, -0.4831), (-0.06793, -0.9413, 0.3307), (-0.4901, 0.3202, 0.8107)	154.9, 4.082, 35.89

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Protein , 1 types, 4 molecules ABCD

#1: Protein	UDP-GLUCOSE DEHYDROGENASE / BCEC Mass: 52219.891 Da / Num. of mol.: 4 / Mutation: YES 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

#1: Protein

UDP-GLUCOSE DEHYDROGENASE / BCEC

Mass: 52219.891 Da / Num. of mol.: 4 / Mutation: YES
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 , 6 types, 1334 molecules

#2: Chemical	ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID / Uridine diphosphate glucuronic acid Mass: 580.285 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₂O₁₈P₂
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1304 / Source method: isolated from a natural source / Formula: H₂O

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Details

Compound details	ENGINEERED RESIDUE IN CHAIN A, TYR 10 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 10 TO SER ...ENGINEERED RESIDUE IN CHAIN A, TYR 10 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 10 TO SER ENGINEERED RESIDUE IN CHAIN C, TYR 10 TO SER ENGINEERED RESIDUE IN CHAIN D, TYR 10 TO SER
Sequence details	CRYSTALLIZED BCEC_Y10S ALSO CONTAINS ADDITIONAL N-TERMINAL TAG HHHHHHGS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 47.5 % / 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 SULFATE, 100 MM SODIUM ACETATE PH 4.5, 11-14 % (W/V) PEG 4K, AND 50 MM NAF), EQUILIBRATED AGAINST 500 MICRO-LITER PRECIPITATION SOLUTION IN THE WELL.

Crystal

Density Matthews: 2.37 Å³/Da / Density % sol: 47.5 % / 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: 1.7→47.4 Å / Num. obs: 217359 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / B_iso Wilson estimate: 17.14 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 7.6
Reflection shell	Resolution: 1.7→1.79 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NATIVE BCEC, PDB ENTRY 2Y0E ,WITH TYR 10 TRUNCATED TO ALA.

2y0e

Resolution: 1.75→42.32 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 13.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1971	9944	5 %
R_work	0.1633	-	-
obs	0.1649	199289	99.7 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.951 Å² / k_sol: 0.384 e/Å³

Displacement parameters

B_iso mean: 24.2 Å²

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

Refinement step

Cycle: LAST / Resolution: 1.75→42.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14042	0	282	1304	15628

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	14947
X-RAY DIFFRACTION	f_angle_d	1.299	20261
X-RAY DIFFRACTION	f_dihedral_angle_d	13.24	5625
X-RAY DIFFRACTION	f_chiral_restr	0.102	2253
X-RAY DIFFRACTION	f_plane_restr	0.005	2646

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	0.2732	368	0.241	6215	X-RAY DIFFRACTION	100
1.7699-1.7907	0.2668	338	0.2347	6248	X-RAY DIFFRACTION	100
1.7907-1.8126	0.2693	328	0.2245	6287	X-RAY DIFFRACTION	100
1.8126-1.8355	0.2593	327	0.2112	6263	X-RAY DIFFRACTION	100
1.8355-1.8597	0.2416	345	0.1994	6236	X-RAY DIFFRACTION	100
1.8597-1.8851	0.2134	330	0.1836	6282	X-RAY DIFFRACTION	100
1.8851-1.9121	0.2038	340	0.1735	6262	X-RAY DIFFRACTION	100
1.9121-1.9406	0.2149	306	0.1698	6326	X-RAY DIFFRACTION	100
1.9406-1.9709	0.2192	312	0.1729	6303	X-RAY DIFFRACTION	100
1.9709-2.0032	0.2083	312	0.1614	6262	X-RAY DIFFRACTION	100
2.0032-2.0378	0.188	316	0.1582	6315	X-RAY DIFFRACTION	100
2.0378-2.0748	0.2068	352	0.1561	6263	X-RAY DIFFRACTION	100
2.0748-2.1148	0.2	329	0.1528	6319	X-RAY DIFFRACTION	100
2.1148-2.1579	0.1868	324	0.1505	6275	X-RAY DIFFRACTION	100
2.1579-2.2048	0.1723	354	0.1458	6290	X-RAY DIFFRACTION	100
2.2048-2.2561	0.1947	327	0.1462	6298	X-RAY DIFFRACTION	100
2.2561-2.3125	0.1807	358	0.1432	6310	X-RAY DIFFRACTION	100
2.3125-2.3751	0.1898	319	0.1504	6311	X-RAY DIFFRACTION	100
2.3751-2.4449	0.2049	310	0.1547	6308	X-RAY DIFFRACTION	100
2.4449-2.5238	0.1933	324	0.1519	6334	X-RAY DIFFRACTION	100
2.5238-2.614	0.1951	341	0.158	6324	X-RAY DIFFRACTION	100
2.614-2.7187	0.1948	332	0.161	6342	X-RAY DIFFRACTION	100
2.7187-2.8424	0.2043	333	0.1634	6321	X-RAY DIFFRACTION	100
2.8424-2.9922	0.2163	323	0.1627	6362	X-RAY DIFFRACTION	100
2.9922-3.1796	0.203	366	0.1622	6360	X-RAY DIFFRACTION	100
3.1796-3.425	0.1707	316	0.1541	6381	X-RAY DIFFRACTION	100
3.425-3.7695	0.1745	372	0.1483	6333	X-RAY DIFFRACTION	99
3.7695-4.3145	0.1658	315	0.1449	6416	X-RAY DIFFRACTION	99
4.3145-5.434	0.1713	325	0.1494	6456	X-RAY DIFFRACTION	99
5.434-42.3323	0.2275	302	0.2101	6342	X-RAY DIFFRACTION	94

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	0.3824	-0.1804	0.2972	0.6623	0.0471	0.9303	-0.0511	0.0531	0.0999	-0.1018	0.0054	0.2442	-0.0774	0.0397	-0.0004	0.1293	-0.0031	-0.0341	0.1032	0.0255	0.1474	57.743	10.0738	-7.5946
2	0.6457	-0.2677	0.2311	0.8254	-0.2894	1.2278	0.0338	0.116	0.0135	-0.1145	-0.0342	0.0631	0.0989	0.2031	-0.0032	0.0799	0.0043	-0.0024	0.1226	0.0064	0.0499	66.5798	-1.8312	-7.6256
3	0.4476	-0.1698	0.0519	0.2488	-0.0461	0.2277	0.0216	-0.0141	-0.027	-0.0406	0.0128	0.0568	-0.0004	-0.0758	0.0912	0.024	0.0051	-0.008	0.0639	0.0026	0.0667	57.1891	-8.9725	17.722
4	0.9439	-0.2237	-0.3649	0.7794	0.5074	1.351	0.0185	-0.1356	0.2078	-0.0603	-0.0717	0.061	-0.0729	-0.1444	-0.0139	0.0103	0.0338	0.0041	0.1137	-0.0366	0.1178	39.405	6.5133	24.5868
5	0.7066	-0.4779	0.4578	0.2702	-0.1327	0.4589	0.0147	-0.1649	-0.4067	0.1573	0.0617	-0.2326	-0.0499	-0.0055	0.0317	0.0935	0.0329	-0.0428	0.0977	0.0394	0.19	82.1692	-17.8034	48.693
6	1.5837	-0.3515	0.9403	0.5796	-0.235	0.8543	-0.1711	-0.2748	-0.0611	0.1833	0.1536	-0.025	-0.163	-0.186	-0.0692	0.1133	0.0619	0.0195	0.1294	0.0059	0.0444	69.1517	-9.6637	47.8919
7	0.1598	-0.1775	0.2106	0.3608	0.007	0.268	0.0041	-0.0275	-0.0384	-0.0226	0.0281	0.0338	0.0439	-0.0522	0.0011	0.0373	0.004	-0.0013	0.0622	0.0074	0.0755	64.2745	-16.4413	21.7679
8	0.457	-0.1795	-0.1001	1.08	0.4036	1.0358	0.0531	-0.0348	-0.0002	-0.0429	0.0558	-0.1531	0.0685	0.098	0.3027	0.0359	0.0098	-0.0132	0.045	-0.0177	0.071	80.5799	-33.2492	14.0493
9	0.5532	-0.1513	0.1849	0.4201	0.3119	0.4691	-0.1647	-0.1715	0.3677	0.0446	-0.1918	0.3752	-0.0895	-0.2943	-0.0187	0.1355	0.0766	-0.009	0.2671	-0.1747	0.5144	58.6891	31.8253	39.6404
10	1.4229	-0.4221	-0.1244	0.7872	-0.0086	0.5119	-0.2252	-0.38	0.157	0.2534	0.0025	0.3718	0.0879	-0.1977	-0.0548	0.1535	0.0626	0.0861	0.1875	-0.0797	0.1875	69.286	24.8436	47.4026
11	0.2535	-0.1864	-0.0724	0.5289	-0.0716	0.4221	-0.0232	-0.019	0.0404	-0.031	0.0206	0.0087	-0.1491	0.0008	0.0297	0.0946	0.0005	-0.0101	0.0377	-0.0063	0.0581	86.7065	24.3806	25.5421
12	0.372	-0.1689	-0.015	2.0956	-0.6954	0.4895	-0.0053	-0.014	0.0118	-0.558	0.0541	0.2491	0.0902	-0.0259	0.1057	0.2564	-0.0058	-0.1029	0.0496	-0.0004	0.0954	76.8719	36.0339	6.5314
13	0.5044	-0.256	-0.5473	0.7885	-0.26	1.0217	-0.2025	-0.1382	-0.1229	0.0009	-0.0692	-0.2718	0.3379	0.1941	-0.0507	0.1306	0.0374	0.0578	0.1163	0.0486	0.1682	105.15	-10.7108	13.1309
14	0.3161	-0.1224	-0.47	1.2695	0.0894	0.6507	-0.0273	0.0183	-0.0322	-0.116	-0.0404	-0.0523	-0.0211	-0.019	-0.151	0.0352	-0.0134	0.0208	0.0447	-0.0091	0.0361	98.5748	1.1944	4.9504
15	0.1647	-0.1725	-0.0845	0.42	0.244	0.3023	-0.0155	-0.0257	-0.0109	-0.043	0.0244	-0.0187	-0.0548	0.052	0.0188	0.0674	-0.0049	-0.0006	0.0633	-0.0058	0.0533	95.0226	16.8863	28.0733
16	0.8182	-0.0159	0.6115	0.3375	0.0691	1.8175	0.0231	-0.0565	-0.0563	0.0659	0.1121	-0.1406	0.1888	0.1672	0.1778	0.0287	0.0406	-0.0117	0.0512	0.014	-0.0354	105.6414	6.6323	47.7924

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 (CHAIN A AND 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 (CHAIN B AND 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 (CHAIN C AND 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 (CHAIN D AND RESID 1501)

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 1334 molecules

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Details

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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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About Yorodumi

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Yorodumi