+Open data
-Basic information
Entry | Database: PDB / ID: 5w6z | |||||||||
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Title | Crystal structure of the H24W mutant of HsNUDT16 | |||||||||
Components | U8 snoRNA-decapping enzyme | |||||||||
Keywords | HYDROLASE / nudix / nudix hydrolase / decapping enzyme / demodification of parylation | |||||||||
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 / dITP diphosphatase activity / phosphodiesterase decapping endonuclease 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 / dITP diphosphatase activity / phosphodiesterase decapping endonuclease 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 / chloride ion binding / snoRNA binding / cobalt ion binding / mRNA catabolic process / manganese ion binding / mRNA binding / nucleotide 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 | 5w6z.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w6z.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 5w6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w6z_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
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Full document | 5w6z_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | 5w6z_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 5w6z_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/5w6z ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w6z | HTTPS FTP |
-Related structure data
Related structure data | 5vy2C 5w6xSC 5wjiC 6b09C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21378.486 Da / Num. of mol.: 4 / Mutation: A22V, H24W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli K-12 (bacteria) / 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: 2.31 Å3/Da / Density % sol: 46.76 % / Mosaicity: 0.568 ° / Mosaicity esd: 0.008 ° |
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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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 21134 / % possible obs: 90.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.083 / Rrim(I) all: 0.15 / Χ2: 2.605 / Net I/σ(I): 8 / Num. measured all: 64806 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W6X Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.84 / SU B: 16.157 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.446 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: 129.68 Å2 / Biso mean: 45.342 Å2 / Biso min: 13.48 Å2
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Refinement step | Cycle: final / Resolution: 2.61→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.611→2.678 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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