+Open data
-Basic information
Entry | Database: PDB / ID: 7r0d | ||||||
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Title | Structure of NUDT15 in complex with Geranyl monophosphate | ||||||
Components | Probable 8-oxo-dGTP diphosphatase NUDT15 | ||||||
Keywords | HYDROLASE / NUDT15 / NUDIX / MTH2 / terpenes | ||||||
Function / homology | Function and homology information nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / Azathioprine ADME / regulation of proteasomal protein catabolic process / xenobiotic catabolic process / response to reactive oxygen species / mitotic cell cycle / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Scaletti, E.R. / Stenmark, P. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: To Be Published Title: Structure of NUDT15 in complex with Geranyl monophosphate Authors: Scaletti, E.R. / Stenmark, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r0d.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r0d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7r0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/7r0d ftp://data.pdbj.org/pub/pdb/validation_reports/r0/7r0d | HTTPS FTP |
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-Related structure data
Related structure data | 5lpgS S: Starting model for refinement |
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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: 18635.002 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT15, MTH2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NV35, nucleotide diphosphatase #2: Chemical | #3: Chemical | #4: 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: 2.04 Å3/Da / Density % sol: 39.76 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 30 % PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→46.64 Å / Num. obs: 34417 / % possible obs: 99.7 % / Redundancy: 11.3 % / CC1/2: 0.998 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 1759 / CC1/2: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LPG Resolution: 1.7→45.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.407 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.112 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.836 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→45.5 Å
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Refine LS restraints |
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LS refinement shell |
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