+Open data
-Basic information
Entry | Database: PDB / ID: 8db6 | ||||||
---|---|---|---|---|---|---|---|
Title | Adenosine/guanosine nucleoside hydrolase | ||||||
Components | Inosine-uridine preferring nucleoside hydrolase family protein | ||||||
Keywords | HYDROLASE / Nucleoside / Adenosine / Guanosine / Parasitic / Inhibitor | ||||||
Function / homology | purine nucleosidase activity / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / purine nucleoside catabolic process / metal ion binding / cytosol / Inosine-uridine preferring nucleoside hydrolase family protein Function and homology information | ||||||
Biological species | Trichomonas vaginalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Muellers, S.N. / Allen, K.N. / Stockman, B.J. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2022 Title: Structure-Guided Insight into the Specificity and Mechanism of a Parasitic Nucleoside Hydrolase. Authors: Muellers, S.N. / Nyitray, M.M. / Reynarowych, N. / Saljanin, E. / Benzie, A.L. / Schoenfeld, A.R. / Stockman, B.J. / Allen, K.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8db6.cif.gz | 247.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8db6.ent.gz | 195.6 KB | Display | PDB format |
PDBx/mmJSON format | 8db6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8db6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8db6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8db6_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 8db6_validation.cif.gz | 65.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/8db6 ftp://data.pdbj.org/pub/pdb/validation_reports/db/8db6 | HTTPS FTP |
-Related structure data
Related structure data | 8db7C 8db8C 8db9C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33476.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_213720 / Production host: Escherichia coli (E. coli) / References: UniProt: A2EYV3 #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium sulfate, 25% PEG-3350, and 0.1 M Bis-tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→29.65 Å / Num. obs: 76440 / % possible obs: 96.77 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.81 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.052 / Rrim(I) all: 0.1 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.02→2.092 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6752 / CC1/2: 0.707 / Rpim(I) all: 0.369 / Rrim(I) all: 0.717 / % possible all: 85.72 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold model Resolution: 2.02→29.65 Å / SU ML: 0.257 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.1265 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→29.65 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|