+Open data
-Basic information
Entry | Database: PDB / ID: 7q74 | ||||||
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Title | Structure of Pla1 apo, with a C-terminal deletion | ||||||
Components | Poly(A) polymerase pla1 | ||||||
Keywords | TRANSFERASE / PolyA polymerase | ||||||
Function / homology | Function and homology information nuclear exosome focus / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / RNA binding / nucleoplasm / ATP binding ...nuclear exosome focus / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.599 Å | ||||||
Authors | Soni, K. / Wild, K. / Sinning, I. | ||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Authors: Soni, K. / Sivadas, A. / Horvath, A. / Dobrev, N. / Hayashi, R. / Kiss, L. / Simon, B. / Wild, K. / Sinning, I. / Fischer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q74.cif.gz | 211.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q74.ent.gz | 168.7 KB | Display | PDB format |
PDBx/mmJSON format | 7q74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q74_validation.pdf.gz | 415.7 KB | Display | wwPDB validaton report |
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Full document | 7q74_full_validation.pdf.gz | 420.1 KB | Display | |
Data in XML | 7q74_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 7q74_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/7q74 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/7q74 | HTTPS FTP |
-Related structure data
Related structure data | 7q72C 7q73C 2hhpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 62718.867 Da / Num. of mol.: 2 / Mutation: C-terminal deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: pla1, SPBC646.04 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q10295, polynucleotide adenylyltransferase #2: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M sodium formate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 25, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.599→57.351 Å / Num. obs: 34690 / % possible obs: 96.8 % / Redundancy: 3.45 % / CC1/2: 0.991 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.178 / Χ2: 0.935 / Net I/σ(I): 7.53 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HHP Resolution: 2.599→57.351 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 32.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.66 Å2 / Biso mean: 64.4718 Å2 / Biso min: 27.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.599→57.351 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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