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Yorodumi- PDB-8osc: Structure of Homo sapiens 2'-deoxynucleoside 5'-phosphate N-hydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8osc | ||||||
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Title | Structure of Homo sapiens 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) bound to deoxyuridine 5'- monophosphate | ||||||
Components | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | ||||||
Keywords | HYDROLASE / deoxyribonucleoside 5'-monophosphate N-glycosidase activity | ||||||
Function / homology | Function and homology information deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / purine nucleotide catabolic process / nucleoside salvage / Purine catabolism / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome ...deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / purine nucleotide catabolic process / nucleoside salvage / Purine catabolism / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Devi, S. / da Silva, R.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Human 2'-Deoxynucleoside 5'-Phosphate N -Hydrolase 1: Mechanism of 2'-Deoxyuridine 5'-Monophosphate Hydrolysis. Authors: Devi, S. / Carberry, A.E. / Zickuhr, G.M. / Dickson, A.L. / Harrison, D.J. / da Silva, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8osc.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8osc.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 8osc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8osc_validation.pdf.gz | 867.2 KB | Display | wwPDB validaton report |
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Full document | 8osc_full_validation.pdf.gz | 869 KB | Display | |
Data in XML | 8osc_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 8osc_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/8osc ftp://data.pdbj.org/pub/pdb/validation_reports/os/8osc | HTTPS FTP |
-Related structure data
Related structure data | 8os9C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16194.220 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: O43598, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds #2: Chemical | ChemComp-UMP / | #3: 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: 1.84 Å3/Da / Density % sol: 33.04 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4 Details: [40 mM sodium propionate, 20 mM MES and 40 mM BIS-TRIS propane] pH 4.0 and 20% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2022 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→33.38 Å / Num. obs: 44559 / % possible obs: 99.7 % / Redundancy: 15.4 % / Biso Wilson estimate: 19.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.015 / Rrim(I) all: 0.06 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 4 / Num. unique obs: 2097 / CC1/2: 0.899 / Rpim(I) all: 0.254 / Rrim(I) all: 0.855 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→33.38 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→33.38 Å
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Refine LS restraints |
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LS refinement shell |
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