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Yorodumi- PDB-5jp4: Crystal structure of S. pombe Dcp1 in complex with the decapping ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jp4 | ||||||
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Title | Crystal structure of S. pombe Dcp1 in complex with the decapping enhancer EDC | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / EVH1 / complex / mRNA / decapping / Hydrolase | ||||||
Function / homology | Function and homology information mRNA phosphatase activator activity / : / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-dependent decapping of nuclear-transcribed mRNA / : / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / meiotic cell cycle / P-body / mRNA processing ...mRNA phosphatase activator activity / : / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-dependent decapping of nuclear-transcribed mRNA / : / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / meiotic cell cycle / P-body / mRNA processing / cytoplasmic stress granule / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.043 Å | ||||||
Authors | Wurm, J.P. / Sprangers, R. | ||||||
Citation | Journal: Rna / Year: 2016 Title: The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface. Authors: Wurm, J.P. / Overbeck, J. / Sprangers, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jp4.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jp4.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 5jp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/5jp4 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/5jp4 | HTTPS FTP |
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-Related structure data
Related structure data | 2qklS 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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Unit cell |
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-Components
#1: Protein | Mass: 15130.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: dcp1, SPBC3B9.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P805 |
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#2: Protein/peptide | Mass: 4212.566 Da / Num. of mol.: 1 / Fragment: UNP Residues 156-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: SPAC18G6.09c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10108 |
#3: Water | ChemComp-HOH / |
-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: 46.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1 M NaCl, 100 mM NaCitrate pH 5-6 / PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→47.813 Å / Num. obs: 10434 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.04→2.15 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QKL Resolution: 2.043→47.813 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.043→47.813 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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