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Yorodumi- PDB-5w0x: Crystal structure of mouse TOR signaling pathway regulator-like (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w0x | ||||||
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Title | Crystal structure of mouse TOR signaling pathway regulator-like (TIPRL) delta 94-103 | ||||||
Components | TIP41-like protein | ||||||
Keywords | SIGNALING PROTEIN / Butterfly-like fold Protein phosphotase 2A regulator | ||||||
Function / homology | TIP41-like protein / TIP41-like family / regulation of phosphoprotein phosphatase activity / negative regulation of phosphoprotein phosphatase activity / TOR signaling / DNA damage checkpoint signaling / cytosol / TIP41-like protein Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.717 Å | ||||||
Authors | Wu, C. / Zheng, A. / Li, J. / Satyshur, K. / Xing, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Methylation-regulated decommissioning of multimeric PP2A complexes. Authors: Wu, C.G. / Zheng, A. / Jiang, L. / Rowse, M. / Stanevich, V. / Chen, H. / Li, Y. / Satyshur, K.A. / Johnson, B. / Gu, T.J. / Liu, Z. / Xing, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w0x.cif.gz | 97 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w0x.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 5w0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/5w0x ftp://data.pdbj.org/pub/pdb/validation_reports/w0/5w0x | HTTPS FTP |
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-Related 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: 28190.967 Da / Num. of mol.: 1 / Fragment: UNP residues 12-259 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tiprl / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BH58 |
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#2: 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: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Cacodylate pH6.5 15% PEG1000(v/v) 0.2M Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2015 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.717→48.495 Å / Num. obs: 12335 / % possible obs: 97.3 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.041 / Net I/σ(I): 31.94 |
Reflection shell | Resolution: 2.717→2.78 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 296 / Rpim(I) all: 0.266 / % possible all: 45.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.717→48.495 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 34.79 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.717→48.495 Å
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Refine LS restraints |
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LS refinement shell |
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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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