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Yorodumi- PDB-8db7: Adenosine/guanosine nucleoside hydrolase bound to a fragment inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 8db7 | ||||||
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Title | Adenosine/guanosine nucleoside hydrolase bound to a fragment inhibitor | ||||||
Components | Inosine-uridine preferring nucleoside hydrolase family protein | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / Nucleoside / Hydrolase / Adenosine / Guanosine / Parasitic / Inhibitor / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | purine nucleosidase activity / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / purine nucleoside catabolic process / cytosol / Chem-R2O / Inosine-uridine preferring nucleoside hydrolase family protein Function and homology information | ||||||
Biological species | Trichomonas vaginalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Muellers, S.N. / Allen, K.N. / Stockman, B.J. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8db7.cif.gz | 248.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8db7.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 8db7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/8db7 ftp://data.pdbj.org/pub/pdb/validation_reports/db/8db7 | HTTPS FTP |
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-Related structure data
Related structure data | 8db6C 8db8C 8db9C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-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: 48.02 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→29.99 Å / Num. obs: 51489 / % possible obs: 98.15 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.1 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.073 / Rrim(I) all: 0.19 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.33→2.413 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5011 / CC1/2: 0.839 / Rpim(I) all: 0.304 / Rrim(I) all: 0.775 / % possible all: 95.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold model Resolution: 2.33→29.99 Å / SU ML: 0.3539 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.3254 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→29.99 Å
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Refine LS restraints |
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LS refinement shell |
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