+Open data
-Basic information
Entry | Database: PDB / ID: 4j0w | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of U3-55K | ||||||
Components | U3 small nucleolar RNA-interacting protein 2 | ||||||
Keywords | RNA BINDING PROTEIN / Beta-Propeller / WD domain / preribosome | ||||||
Function / homology | Function and homology information box C/D methylation guide snoRNP complex / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / small-subunit processome / ribosomal small subunit biogenesis / rRNA processing / nucleolus / RNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Zhang, L. / Lin, J. / Ye, K. | ||||||
Citation | Journal: Rna / Year: 2013 Title: Structural and functional analysis of the U3 snoRNA binding protein Rrp9. Authors: Zhang, L. / Lin, J. / Ye, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4j0w.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4j0w.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 4j0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/4j0w ftp://data.pdbj.org/pub/pdb/validation_reports/j0/4j0w | HTTPS FTP |
---|
-Related structure data
Related structure data | 4j0xSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: RRP9, RNU3IP2, U355K / Plasmid: pFastBac / Cell line (production host): HIGH FIVE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43818 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.56 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
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: 0.9792 Å / Relative weight: 1 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|