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Open data
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Basic information
Entry | Database: PDB / ID: 4r3h | ||||||
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Title | The crystal structure of an apo RNA binding protein | ||||||
![]() | YTH domain-containing protein 1 | ||||||
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Function / homology | ![]() primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, C. / Liu, K. / Tempel, W. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain. Authors: Xu, C. / Wang, X. / Liu, K. / Roundtree, I.A. / Tempel, W. / Li, Y. / Lu, Z. / He, C. / Min, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.5 KB | Display | ![]() |
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PDB format | ![]() | 108.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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: 18823.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-UNX / #3: Chemical | ChemComp-SO4 / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.7 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 5, 2014 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→27.31 Å / Num. obs: 28931 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Details: Structure of an isomorphous crystal was solved by molecular replacement using PHASER and coordinates from PDB entry 2YUD. Phase improvement and automated model building were performed with ...Details: Structure of an isomorphous crystal was solved by molecular replacement using PHASER and coordinates from PDB entry 2YUD. Phase improvement and automated model building were performed with ARP/WARP. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.28 Å2 / Biso mean: 32.1817 Å2 / Biso min: 15.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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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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