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- PDB-6r9o: Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r9o | |||||||||
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Title | Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGA RNA | |||||||||
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![]() | HYDROLASE / DEDD RNase / deadenylase / pseudoubiquitin hydrolase | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Tang, T.T.L. / Stowell, J.A.W. / Hill, C.H. / Passmore, L.A. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.7 KB | Display | ![]() |
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PDB format | ![]() | 203.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.4 KB | Display | ![]() |
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Full document | ![]() | 458.1 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r9iC ![]() 6r9jC ![]() 6r9mC ![]() 6r9pC ![]() 6r9qC ![]() 4czwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 1633.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in all eukaryotes. / Source: (synth.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.31 Å3/Da / Density % sol: 71.46 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2018 |
Radiation | Monochromator: Single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 3.319→85.565 Å / Num. obs: 20744 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.319→3.41 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.98 / Mean I/σ(I) obs: 1 / Num. unique obs: 1496 / CC1/2: 0.624 / % possible all: 99.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CZW Resolution: 3.319→85.565 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 366.9 Å2 / Biso mean: 159.1017 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.319→85.565 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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