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Yorodumi- PDB-3md3: Crystal Structure of the First Two RRM Domains of Yeast Poly(U) B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3md3 | ||||||
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Title | Crystal Structure of the First Two RRM Domains of Yeast Poly(U) Binding Protein (Pub1) | ||||||
Components | Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 | ||||||
Keywords | RNA BINDING PROTEIN / RRM / RNP / RBD / poly(U) binding / tandem / Acetylation / Cytoplasm / Nucleus / RNA-binding | ||||||
Function / homology | Function and homology information poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / stress granule assembly / regulation of mRNA stability / P-body / cytoplasmic stress granule / mRNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Li, H. / Shi, H. / Zhu, Z. / Wang, H. / Niu, L. / Teng, M. | ||||||
Citation | Journal: To be published Title: Crystal Structure of the First Two RRM Domains of Yeast Poly(U) Binding Protein (Pub1) Authors: Li, H. / Shi, H. / Zhu, Z. / Wang, H. / Niu, L. / Teng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3md3.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3md3.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 3md3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/3md3 ftp://data.pdbj.org/pub/pdb/validation_reports/md/3md3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 18793.803 Da / Num. of mol.: 1 / Fragment: N-terminal two RRM domains / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32588 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: 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: 3.02 Å3/Da / Density % sol: 59.3 % / Mosaicity: 0.385 ° |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.0M ammonium sulfate, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 22, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 7092 / % possible obs: 99.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.117 / Χ2: 1.202 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.9 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.817 / SU R Cruickshank DPI: 1.008 / SU Rfree: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.008 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.58 Å2 / Biso mean: 19.472 Å2 / Biso min: 2.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→49.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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