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Open data
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Basic information
Entry | Database: PDB / ID: 3nil | ||||||
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Title | The structure of UBR box (RDAA) | ||||||
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![]() | METAL BINDING PROTEIN / E3 ubiquitin ligase / UBR box / Zinc-binding protein / N-end rule / Ligase | ||||||
Function / homology | ![]() regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / protein monoubiquitination ...regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / protein monoubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / ERAD pathway / ubiquitin ligase complex / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Choi, W.S. / Jeong, B.-C. / Lee, M.-R. / Song, H.K. | ||||||
![]() | ![]() Title: Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases Authors: Choi, W.S. / Jeong, B.-C. / Joo, Y.J. / Lee, M.-R. / Kim, J. / Eck, M.J. / Song, H.K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.1 KB | Display | ![]() |
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Full document | ![]() | 470.8 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nihC ![]() 3niiC ![]() 3nijC ![]() 3nikC ![]() 3nimC ![]() 3ninC ![]() 3nisSC ![]() 3nitC C: citing same article ( S: Starting model for refinement |
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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: 9236.394 Da / Num. of mol.: 4 / Fragment: UBR-type domain, residues 115-194 Source method: isolated from a genetically manipulated source Details: UBR box Source: (gene. exp.) ![]() ![]() Plasmid: pET / Production host: ![]() ![]() #2: Protein/peptide | | Mass: 432.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.89 % / Mosaicity: 0.488 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Bis-Tris pH 5.5, 0.2M ammonium acetate, 25%(w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 30761 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.064 / Χ2: 1.394 / Net I/σ(I): 10.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NIS Resolution: 1.75→38.38 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.788 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 99.98 Å2 / Biso mean: 31.4541 Å2 / Biso min: 15.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→38.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.749→1.795 Å / Total num. of bins used: 20
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