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Yorodumi- PDB-6r9j: Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r9j | |||||||||
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Title | Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with A7 RNA | |||||||||
Components |
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Keywords | HYDROLASE / DEDD RNase / deadenylase / pseudoubiquitin hydrolase | |||||||||
Function / homology | Function and homology information PAN complex / Deadenylation of mRNA / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / postreplication repair / P-body / mRNA processing / nucleic acid binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.326 Å | |||||||||
Authors | Tang, T.T.L. / Stowell, J.A.W. / Hill, C.H. / Passmore, L.A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2019 Title: The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases. Authors: Tang, T.T.L. / Stowell, J.A.W. / Hill, C.H. / Passmore, L.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r9j.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r9j.ent.gz | 203.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/6r9j ftp://data.pdbj.org/pub/pdb/validation_reports/r9/6r9j | HTTPS FTP |
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-Related structure data
Related structure data | 6r9iC 6r9mC 6r9oC 6r9pC 6r9qC 4czwS 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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Unit cell |
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-Components
#1: Protein | Mass: 77776.102 Da / Num. of mol.: 1 / Mutation: E912A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: PAN2, YGL094C / Plasmid: pACEBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53010, poly(A)-specific ribonuclease |
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#2: RNA chain | Mass: 2259.483 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in all eukaryotic organisms. Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.32 Å3/Da / Density % sol: 71.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.4 M ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2018 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.326→71.928 Å / Num. obs: 20507 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.326→3.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.821 / Mean I/σ(I) obs: 1 / Num. unique obs: 1481 / CC1/2: 0.59 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CZW Resolution: 3.326→71.928 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 343.56 Å2 / Biso mean: 151.0181 Å2 / Biso min: 71.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.326→71.928 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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