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Open data
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Basic information
Entry | Database: PDB / ID: 4j0w | ||||||
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Title | Structure of U3-55K | ||||||
![]() | U3 small nucleolar RNA-interacting protein 2 | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() box C/D methylation guide snoRNP complex / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, L. / Lin, J. / Ye, K. | ||||||
![]() | ![]() Title: Structural and functional analysis of the U3 snoRNA binding protein Rrp9. Authors: Zhang, L. / Lin, J. / Ye, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.3 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4j0xSC S: Starting model for refinement C: citing same article ( |
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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: 37443.613 Da / Num. of mol.: 1 / Fragment: WD DOMAIN, UNP RESIDUES 137-475 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion / pH: 8 Details: 100mM HEPES-K, 25% (v/v) ethylene glycol, pH 8.0, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→50 Å / Num. obs: 38893 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.7 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 16 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4J0X Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.034 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.615 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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