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Yorodumi- PDB-5n2v: Changes in conformational equilibria regulate the activity of the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n2v | |||||||||
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Title | Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process ...mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process / meiotic cell cycle / P-body / cytoplasmic stress granule / mRNA processing / manganese ion binding / single-stranded RNA binding / magnesium ion binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Holdermann, I. / Sprangers, R. | |||||||||
Funding support | 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme. Authors: Wurm, J.P. / Holdermann, I. / Overbeck, J.H. / Mayer, P.H.O. / Sprangers, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n2v.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n2v.ent.gz | 129.4 KB | Display | PDB format |
PDBx/mmJSON format | 5n2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n2v_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5n2v_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5n2v_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 5n2v_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/5n2v ftp://data.pdbj.org/pub/pdb/validation_reports/n2/5n2v | HTTPS FTP |
-Related structure data
Related structure data | 5j3tS 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: 15130.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: dcp1, SPBC3B9.21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P805 #2: Protein | Mass: 28689.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: dcp2, SPAC19A8.12 / Production host: Escherichia coli (E. coli) / References: UniProt: O13828, Hydrolases #3: Protein/peptide | Mass: 2742.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10108 #4: Chemical | ChemComp-MG / #5: Chemical | |
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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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 41% M1K3350 Morpheus Mix 4, MOPS pH 7.0, 0.06 M MgCl2/CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.3 Å / Num. obs: 15440 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.95 / Rmerge(I) obs: 0.24 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.64 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5j3t Resolution: 3.1→48.289 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→48.289 Å
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Refine LS restraints |
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LS refinement shell |
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