[English] 日本語
![](img/lk-miru.gif)
- PDB-8oia: Trichomonas vaginalis riboside hydrolase in complex with D-ribose -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8oia | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Trichomonas vaginalis riboside hydrolase in complex with D-ribose | |||||||||
![]() | Inosine-uridine preferring nucleoside hydrolase family protein | |||||||||
![]() | HYDROLASE / NH-fold / nucleoside hydrolase / riboside hydrolase / nicotinamide riboside | |||||||||
Function / homology | ![]() purine nucleosidase activity / purine nucleoside catabolic process / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Patrone, M. / Stockman, B.J. / Degano, M. | |||||||||
Funding support | ![]() ![]()
| |||||||||
![]() | ![]() Title: A riboside hydrolase that salvages both nucleobases and nicotinamide in the auxotrophic parasite Trichomonas vaginalis. Authors: Patrone, M. / Galasyn, G.S. / Kerin, F. / Nyitray, M.M. / Parkin, D.W. / Stockman, B.J. / Degano, M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 704.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 444.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 48.4 KB | Display | |
Data in CIF | ![]() | 66.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oi7C ![]() 8oi9C ![]() 8oibC ![]() 8oicC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 346 / Label seq-ID: 2 - 346
NCS ensembles :
|
-
Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/RIB.gif)
![](data/chem/img/RIB.gif)
#1: Protein | Mass: 39206.977 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Sugar | ChemComp-RIB / |
---|
-Non-polymers , 4 types, 116 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.85 Details: 200 mM ammonium citrate dibasic pH 4.85, 15% PEG 3300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 10, 2021 |
Radiation | Monochromator: Silicon crystal 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→43.981 Å / Num. obs: 71792 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.981 / Rpim(I) all: 0.136 / Rsym value: 0.305 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4593 / CC1/2: 0.425 / Rpim(I) all: 0.425 / Rsym value: 1.608 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.968 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→43.981 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|