PDB-5idt: Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase ...

ID or keywords:

Entry

Database: PDB / ID: 5idt

Title

Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Burkholderia vietnamiensis with bound Thymidine

Components

Glucose-1-phosphate thymidylyltransferase

Keywords

TRANSFERASE / SSGCID /

Glucose-1-phosphate thymidylyltransferase /

Burkholderia vietnamiensis /

Nucleotidyltransferase /

Thymidine /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

glucose-1-phosphate thymidylyltransferase /

glucose-1-phosphate thymidylyltransferase activity / extracellular polysaccharide biosynthetic process /

metal ion binding
Similarity search - Function

Biological species

Burkholderia vietnamiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.35 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Burkholderia vietnamiensis with bound Thymidine
Authors: Dranow, D.M. / Hornayi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Feb 24, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5idt.cif.gz	446.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5idt.ent.gz	364.7 KB	Display	PDB format
PDBx/mmJSON format	5idt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/id/5idt ftp://data.pdbj.org/pub/pdb/validation_reports/id/5idt	HTTPS FTP

-
Related structure data

Related structure data	1fxoS S: Starting model for refinement
Similar structure data	5ids-1 3pkp-6 5ids-2 3pkq-3 3pkp-3 1mp4-d 3gak-d 6e2m-d 5nyj-10 6no3-d 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
Other databases	TargetTrack: SSGCID-BuviA.00118.c

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Glucose-1-phosphate thymidylyltransferase

B: Glucose-1-phosphate thymidylyltransferase

C: Glucose-1-phosphate thymidylyltransferase

D: Glucose-1-phosphate thymidylyltransferase

hetero molecules

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

1

A: Glucose-1-phosphate thymidylyltransferase

B: Glucose-1-phosphate thymidylyltransferase

hetero molecules

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

2

C: Glucose-1-phosphate thymidylyltransferase

D: Glucose-1-phosphate thymidylyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	112.110, 114.860, 95.780
Angle α, β, γ (deg.)	90.00, 90.58, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Glucose-1-phosphate thymidylyltransferase / Mass: 33318.730 Da / Num. of mol.: 4 / Fragment: BuviA.00118.c.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria) Strain: G4 / LMG 22486 / Gene: Bcep1808_3215 / Plasmid: BuviA.00118.c.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A4JIV2, glucose-1-phosphate thymidylyltransferase
#2: Chemical	ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₂O₅
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.31 Å³/Da / Density % sol: 46.83 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: BuviA.00118.c.B1.PS02537 at 20.28 mg/ml was incubated with 3 mM thymidine, then mixed 1:1 with JCSG+(g4): 0.2 M trimethylamine n-oxide, 20% (w/v) PEG-2000 MME, 0.1M Tris base/HCl, pH = 8.5, ...Details: BuviA.00118.c.B1.PS02537 at 20.28 mg/ml was incubated with 3 mM thymidine, then mixed 1:1 with JCSG+(g4): 0.2 M trimethylamine n-oxide, 20% (w/v) PEG-2000 MME, 0.1M Tris base/HCl, pH = 8.5, cryoprotected with 20% ethylene glycol

Crystal

Density Matthews: 2.31 Å³/Da / Density % sol: 46.83 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BuviA.00118.c.B1.PS02537 at 20.28 mg/ml was incubated with 3 mM thymidine, then mixed 1:1 with JCSG+(g4): 0.2 M trimethylamine n-oxide, 20% (w/v) PEG-2000 MME, 0.1M Tris base/HCl, pH = 8.5, ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2016 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.35→50 Å / Num. obs: 50137 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.84 % / B_iso Wilson estimate: 44.39 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.047 / Net I/σ(I): 20.59

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.35-2.41		0.588	3.08	1	99
2.41-2.48		0.453	3.85	1	99
2.48-2.55		0.345	4.86	1	99
2.55-2.63		0.268	5.95	1	99
2.63-2.71		0.227	6.9	1	99.1
2.71-2.81		0.173	8.71	1	99.3
2.81-2.91		0.13	10.79	1	99.2
2.91-3.03		0.101	13.56	1	99.4
3.03-3.17		0.08	16.61	1	99.4
3.17-3.32		0.058	21.51	1	99.4
3.32-3.5		0.044	26.71	1	99.4
3.5-3.72		0.036	31.68	1	99.4
3.72-3.97		0.03	37.14	1	99.7
3.97-4.29		0.026	43.14	1	99.7
4.29-4.7		0.024	46.71	1	99.5
4.7-5.25		0.023	48.67	1	99.7
5.25-6.07		0.023	47.23	1	99.8
6.07-7.43		0.021	48.98	1	99.9
7.43-10.51		0.019	57.81	1	99
	10.51	0.021	55.97	1	92.8

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_2271: ???)	refinement
XSCALE		data scaling
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1FXO

1fxo

Resolution: 2.35→48.163 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.231	1863	3.72 %
R_work	0.1765	-	-
obs	0.1784	50096	99.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.35→48.163 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8449	0	54	158	8661

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8720
X-RAY DIFFRACTION	f_angle_d	0.991	11920
X-RAY DIFFRACTION	f_dihedral_angle_d	13.705	5095
X-RAY DIFFRACTION	f_chiral_restr	0.059	1339
X-RAY DIFFRACTION	f_plane_restr	0.007	1563

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 (%)
2.35-2.4135	0.3151	142	0.26	3669	X-RAY DIFFRACTION	99
2.4135-2.4845	0.3255	151	0.2356	3674	X-RAY DIFFRACTION	99
2.4845-2.5647	0.2667	122	0.2225	3705	X-RAY DIFFRACTION	99
2.5647-2.6564	0.3028	156	0.2074	3686	X-RAY DIFFRACTION	99
2.6564-2.7627	0.2817	163	0.2134	3678	X-RAY DIFFRACTION	99
2.7627-2.8885	0.267	147	0.2038	3669	X-RAY DIFFRACTION	99
2.8885-3.0407	0.2595	152	0.2007	3684	X-RAY DIFFRACTION	99
3.0407-3.2312	0.2885	154	0.2035	3737	X-RAY DIFFRACTION	99
3.2312-3.4806	0.2275	132	0.1907	3733	X-RAY DIFFRACTION	99
3.4806-3.8308	0.2344	121	0.1756	3739	X-RAY DIFFRACTION	100
3.8308-4.3848	0.1897	148	0.1507	3716	X-RAY DIFFRACTION	100
4.3848-5.5231	0.1911	136	0.1414	3765	X-RAY DIFFRACTION	100
5.5231-48.1736	0.1896	139	0.1559	3778	X-RAY DIFFRACTION	99

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	4.6174	-4.4195	2.5139	4.1282	-2.349	3.1767	-0.1002	0.4108	-0.7501	-0.0155	0.2435	0.0653	-0.2265	0.0002	-0.2363	0.2968	-0.0698	0.0905	0.369	-0.0476	0.3446	22.6331	-0.8037	38.5293
2	5.4608	1.1252	0.8108	5.7125	1.3118	0.3474	-0.3852	0.037	-0.1837	-0.0303	0.471	-0.0026	0.0516	0.1793	-0.1753	0.3532	-0.0302	0.0523	0.5239	0.0178	0.3429	14.3179	7.9001	35.8602
3	1.4235	-0.0306	-0.4194	2.1232	0.0669	3.9286	0.1556	-0.2752	0.2105	0.0727	0.1692	-0.3777	-0.1	0.2567	-0.3029	0.2331	-0.0615	-0.0144	0.405	-0.1077	0.4539	28.4349	2.1169	43.0461
4	2.0815	-0.0089	-0.9971	7.8866	0.9481	2.0459	0.2685	-1.8341	-0.3039	0.7824	0.0769	0.7386	0.8919	-0.8619	-0.2239	0.6068	-0.0807	0.0425	0.916	0.0033	0.5337	16.0666	-11.9906	55.4397
5	3.8202	-2.0035	-2.1954	3.0384	-0.242	4.1318	-0.188	-0.2716	-0.381	0.2197	0.158	-0.1181	0.6147	0.035	0.0118	0.3411	-0.0517	-0.121	0.3906	-0.0162	0.4717	25.9589	-13.624	49.344
6	5.23	0.1675	1.6443	4.155	0.9519	5.2038	0.0295	-0.2668	0.1695	0.3774	0.2811	-0.0386	0.1169	-0.1604	-0.317	0.3406	0.0366	0.0593	0.4404	0.0277	0.3221	10.0644	6.4211	48.9658
7	5.2332	0.5571	-0.3537	3.0854	-0.9979	4.4542	-0.0067	-0.5004	0.7887	-0.1307	0.0605	-0.4933	-0.8398	-0.4295	-0.0356	0.5964	-0.0112	0.0323	0.4583	-0.2296	0.6092	25.1927	21.8995	46.8398
8	6.0422	-2.6883	4.1643	1.2115	-2.0772	6.3541	-0.1227	1.5779	0.8227	-0.1804	-0.1661	-0.1869	-0.8073	0.8806	0.2674	0.5221	0.0357	0.169	0.718	0.1199	0.5214	6.0454	19.7352	23.8426
9	1.8875	-0.1045	-0.0289	1.5282	-0.776	2.1104	0.0994	1.0822	0.4255	-0.4962	0.1177	-0.0923	-0.098	-0.2945	-0.1545	0.5246	0.0933	0.0918	0.9434	0.1783	0.458	0.5606	16.1244	20.3671
10	0.518	0.3971	1.1848	3.9376	-3.1763	7.4637	-0.0348	0.716	1.6641	-0.0265	0.0505	-0.0917	-1.0149	-0.5282	0.0275	0.6971	0.2192	0.096	1.0336	0.4928	1.0204	-6.8684	32.6367	22.4212
11	2.7514	0.8287	0.3947	3.731	0.4101	2.6393	-0.0805	0.1936	0.2697	0.129	0.0778	0.3439	-0.1027	-0.3491	0.0082	0.3496	0.0912	0.0565	0.5358	0.0505	0.3398	-3.2692	14.3097	38.0956
12	3.0462	0.8713	-0.139	4.1585	0.2083	3.9473	-0.0723	0.5956	-0.6043	-0.4403	0.0265	0.0326	0.5375	-0.6186	0.0015	0.5254	-0.0164	-0.0008	0.8128	-0.1093	0.4624	-4.5691	-2.3911	24.7947
13	8.6952	2.3785	2.7536	1.9334	1.4525	1.4573	0.2097	-0.9393	-0.9407	0.127	0.0589	0.0571	0.1654	-0.4435	-0.3	0.4609	-0.1398	0.0927	0.4057	0.0155	0.4664	35.3026	1.4244	13.3921
14	3.778	-4.3914	1.362	8.8791	-4.0977	2.101	-0.2557	-0.1589	-0.248	0.3404	0.081	-0.0071	-0.0523	-0.3601	0.0891	0.4181	-0.1339	0.0824	0.3788	-0.0744	0.3812	43.4369	9.8953	14.3647
15	1.7162	0.6804	-0.1017	2.8212	-1.1595	2.2736	0.0214	-0.0605	0.1056	0.164	0.0687	0.3841	-0.1604	-0.1845	-0.0998	0.3611	-0.1142	0.1305	0.4249	-0.0954	0.5513	29.6893	10.5017	13.5561
16	3.8765	2.9169	1.1151	2.9987	0.0481	7.5774	-0.2101	-0.0216	-0.6666	0.4276	0.5021	-0.0362	0.8988	-0.2808	-0.3307	0.4973	-0.1269	0.1569	0.5511	-0.15	0.6553	25.9157	-0.9076	18.0234
17	2.4206	1.9098	1.0252	3.2925	-0.8225	2.6642	-0.1069	0.4612	-0.575	-0.566	-0.0196	-0.4235	1.1206	-0.2618	0.0507	0.7704	-0.2387	0.1431	0.5467	-0.2085	0.6138	32.6538	-4.3511	-1.9427
18	6.367	1.695	-2.1035	5.0843	-1.9739	4.0014	-0.2481	-0.3929	-0.6625	-0.5301	0.1696	0.0559	0.6567	-0.3996	0.0624	0.5134	-0.2767	0.0864	0.5823	-0.1268	0.6473	26.591	-9.3072	7.7741
19	0.7908	1.3886	-0.4366	2.4437	-0.7788	0.2541	-0.4946	0.5459	-1.2378	-0.3016	-0.0644	-0.2426	1.0183	-0.718	0.1401	0.9873	-0.4728	0.2162	0.701	-0.1973	0.9175	26.804	-11.3244	0.4664
20	3.8766	-0.039	-0.081	0.2479	-0.7183	1.7303	-0.0954	0.316	0.2668	-0.126	0.0782	-0.1191	0.049	-0.0608	-0.0044	0.4385	-0.1078	0.0655	0.3617	-0.0563	0.4486	39.0922	12.7005	1.1533
21	7.7774	-4.2946	-3.0106	5.9781	-2.4933	9.548	-0.1272	-0.6343	0.904	0.726	-0.3116	-0.043	-1.9357	0.7572	0.3947	0.8553	-0.1424	0.0846	0.4496	-0.0177	0.7903	32.8627	27.6606	6.4555
22	4.5731	2.263	2.8579	2.0998	1.0324	4.1471	-0.2821	-0.292	0.4889	0.2346	-0.1097	0.2922	-0.1317	-0.1459	0.4806	0.4103	-0.1202	0.0588	0.3523	-0.0515	0.4088	51.5064	18.1901	21.5559
23	3.1847	0.8682	0.4008	3.3404	0.86	3.2924	0.0888	-0.5324	0.2489	0.3057	-0.282	0.0197	-0.061	-0.0401	0.1559	0.3869	-0.1714	-0.0394	0.5048	-0.067	0.3742	61.8253	24.8993	26.4819
24	0.7906	0.7699	0.4057	2.6749	0.804	2.6095	0.0785	-0.1685	-0.0842	0.2034	-0.1629	-0.3471	-0.0145	0.3473	0.0527	0.3923	-0.1201	0.0275	0.4273	-0.0009	0.4868	64.4103	18.3847	18.5647
25	6.9338	-5.2898	0.4663	4.4613	-1.7667	4.7187	0.0626	0.0957	-1.7506	1.014	-0.6278	0.7247	1.3567	-0.7845	0.3199	0.826	-0.0595	0.0491	0.351	0.0497	0.9782	61.5162	-3.8849	21.8109

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 35 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 156 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 157 through 218 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 219 through 246 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 247 through 290 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 19 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 20 through 139 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 140 through 218 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 219 through 247 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 248 through 290 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 2 through 19 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 20 through 35 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 36 through 76 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 77 through 100 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 101 through 170 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 171 through 199 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 200 through 218 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 219 through 265 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 266 through 290 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 2 through 35 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 36 through 199 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 200 through 265 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 266 through 290 )

-
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://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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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