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Yorodumi- PDB-3aca: Crystal structure of human NUDT5 complexed with 8-oxo-dADP and ma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aca | ||||||
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Title | Crystal structure of human NUDT5 complexed with 8-oxo-dADP and manganese | ||||||
Components | ADP-sugar pyrophosphatase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Nudix motif / Magnesium / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / nucleotide metabolic process / snoRNA binding / nucleotidyltransferase activity / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Arimori, T. / Yamagata, Y. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Diverse substrate recognition and hydrolysis mechanisms of human NUDT5 Authors: Arimori, T. / Tamaoki, H. / Nakamura, T. / Kamiya, H. / Ikemizu, S. / Takagi, Y. / Ishibashi, T. / Harashima, H. / Sekiguchi, M. / Yamagata, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aca.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aca.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 3aca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aca_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3aca_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3aca_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 3aca_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/3aca ftp://data.pdbj.org/pub/pdb/validation_reports/ac/3aca | HTTPS FTP |
-Related structure data
Related structure data | 3ac9C 3l85SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 21700.643 Da / Num. of mol.: 2 / Fragment: residues 13-208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5, HSPC115 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKK9, ADP-ribose diphosphatase #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.1M Sodium Citrate, 30% PEG3350, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2009 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 24799 / Num. obs: 24799 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 28.67 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 37.7 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1212 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3L85 Resolution: 2.05→34.893 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.813 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 25.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.096 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.33 Å2 / Biso mean: 36.447 Å2 / Biso min: 10.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→34.893 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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