+Open data
-Basic information
Entry | Database: PDB / ID: 5vy2 | |||||||||
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Title | Crystal structure of the F36A mutant of HsNUDT16 | |||||||||
Components | U8 snoRNA-decapping enzyme | |||||||||
Keywords | HYDROLASE / nudix / nudix hydrolase / decapping enzyme / demodification of parylation / demodification of marylation / ADPribose / di-ADPribose | |||||||||
Function / homology | Function and homology information inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / dITP diphosphatase activity / negative regulation of rRNA processing ...inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / dITP diphosphatase activity / negative regulation of rRNA processing / NAD-cap decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Phosphate bond hydrolysis by NUDT proteins / metalloexopeptidase activity / cobalt ion binding / chloride ion binding / snoRNA binding / mRNA catabolic process / manganese ion binding / nucleotide binding / mRNA binding / nucleolus / magnesium ion binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | |||||||||
Authors | Thirawatananond, P. / Gabelli, S.B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Rep / Year: 2019 Title: Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. Authors: Thirawatananond, P. / McPherson, R.L. / Malhi, J. / Nathan, S. / Lambrecht, M.J. / Brichacek, M. / Hergenrother, P.J. / Leung, A.K.L. / Gabelli, S.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vy2.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vy2.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vy2 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vy2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21254.330 Da / Num. of mol.: 2 / Mutation: A22V, F36A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIPL References: UniProt: Q96DE0, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase, inosine diphosphate phosphatase #2: Chemical | ChemComp-NA / | #3: 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: 1.95 Å3/Da / Density % sol: 36.79 % / Mosaicity: 1.298 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: PEG 8000, CHES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 13719 / % possible obs: 92 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.055 / Rrim(I) all: 0.09 / Χ2: 4.229 / Net I/σ(I): 20.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdbid XX Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.275 / SU ML: 0.178 / SU R Cruickshank DPI: 0.691 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.691 / ESU R Free: 0.288 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.64 Å2 / Biso mean: 29.92 Å2 / Biso min: 10.67 Å2
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Refinement step | Cycle: final / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.349 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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