+Open data
-Basic information
Entry | Database: PDB / ID: 6wug | ||||||
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Title | Crystal Structure of S. pombe Rai1 in complex with 3'-FADP | ||||||
Components | Decapping nuclease din1 | ||||||
Keywords | HYDROLASE / FAD / 3'-FADP / RNA / cap / decapping / Rai1 | ||||||
Function / homology | Function and homology information 5'-hydroxyl dinucleotide hydrolase activity / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / phosphodiesterase decapping endonuclease activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nuclear-transcribed mRNA catabolic process / mRNA processing ...5'-hydroxyl dinucleotide hydrolase activity / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / phosphodiesterase decapping endonuclease activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nuclear-transcribed mRNA catabolic process / mRNA processing / GDP binding / RNA binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Doamekpor, S.K. / Tong, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs. Authors: Doamekpor, S.K. / Grudzien-Nogalska, E. / Mlynarska-Cieslak, A. / Kowalska, J. / Kiledjian, M. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wug.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wug.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wug_validation.pdf.gz | 899.3 KB | Display | wwPDB validaton report |
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Full document | 6wug_full_validation.pdf.gz | 903 KB | Display | |
Data in XML | 6wug_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 6wug_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/6wug ftp://data.pdbj.org/pub/pdb/validation_reports/wu/6wug | HTTPS FTP |
-Related structure data
Related structure data | 6wufC 6wuiC 6wukC 3fqgS 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: 42971.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: din1, SPAC19D5.06c / Production host: Escherichia coli (E. coli) References: UniProt: O13836, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-UBG / [( | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% (w/v) PEG 3350 and 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.66 Å / Num. obs: 32480 / % possible obs: 94.4 % / Redundancy: 2.011 % / Biso Wilson estimate: 41.63 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.84 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.03 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 1.39 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FQG Resolution: 1.9→48.66 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.82 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.66 Å
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Refine LS restraints |
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LS refinement shell |
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