+Open data
-Basic information
Entry | Database: PDB / ID: 5wu1 | ||||||
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Title | Crystal structure of apo human Tut1, form I | ||||||
Components | Speckle targeted PIP5K1A-regulated poly(A) polymerase | ||||||
Keywords | TRANSFERASE / Terminal nucleotidyl transferase | ||||||
Function / homology | Function and homology information U6 snRNA 3'-end processing / RNA uridylyltransferase / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA uridylyltransferase activity / snRNA processing / mRNA cleavage and polyadenylation specificity factor complex / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / mRNA 3'-end processing / enzyme-substrate adaptor activity ...U6 snRNA 3'-end processing / RNA uridylyltransferase / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA uridylyltransferase activity / snRNA processing / mRNA cleavage and polyadenylation specificity factor complex / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / mRNA 3'-end processing / enzyme-substrate adaptor activity / U6 snRNA binding / mRNA 3'-UTR binding / nuclear speck / nucleolus / enzyme binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Yamashita, S. / Tomita, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Crystal structures of U6 snRNA-specific terminal uridylyltransferase Authors: Yamashita, S. / Takagi, Y. / Nagaike, T. / Tomita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wu1.cif.gz | 397.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wu1.ent.gz | 326.5 KB | Display | PDB format |
PDBx/mmJSON format | 5wu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wu1_validation.pdf.gz | 469.3 KB | Display | wwPDB validaton report |
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Full document | 5wu1_full_validation.pdf.gz | 480.7 KB | Display | |
Data in XML | 5wu1_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 5wu1_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/5wu1 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/5wu1 | HTTPS FTP |
-Related structure data
Related structure data | 5wu2SC 5wu3C 5wu4C 5wu5C 5wu6C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 62253.586 Da / Num. of mol.: 2 / Fragment: UNP residues 141-874 / Mutation: C372A, C399A, C415A, C501A, C504S, C574A Source method: isolated from a genetically manipulated source Details: Sequence of 141-874(C-term) of human Tut1 was cloned to pET22b vector with NdeI and XhoI sites. Residues of 235-304 and 651-750 were deleted for crystallization. C372A, C399A, C415A, C501A, ...Details: Sequence of 141-874(C-term) of human Tut1 was cloned to pET22b vector with NdeI and XhoI sites. Residues of 235-304 and 651-750 were deleted for crystallization. C372A, C399A, C415A, C501A, C504S, and C574A mutations were introduced to improve the crystals. Source: (gene. exp.) Homo sapiens (human) / Gene: TUT1, RBM21 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H6E5, polynucleotide adenylyltransferase, RNA uridylyltransferase #2: Chemical | |
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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: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Hepes pH 7.5, PEG3350, Tacsimate |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 15, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 31837 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 62.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.188 / Net I/σ(I): 10.23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WU2 Resolution: 2.8→19.979 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.32 Å2 / Biso mean: 76.8 Å2 / Biso min: 26.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→19.979 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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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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