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- PDB-7us1: Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules -
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Open data
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Basic information
Entry | Database: PDB / ID: 7us1 | ||||||
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Title | Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules | ||||||
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![]() | LIGASE / Parkin R0RB / R0RB:2pUb / R0RB:pUb | ||||||
Function / homology | ![]() RBR-type E3 ubiquitin transferase / ubiquitin ligase complex / modification-dependent protein catabolic process / ubiquitin-protein transferase activity / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / mitochondrion / nucleus / metal ion binding ...RBR-type E3 ubiquitin transferase / ubiquitin ligase complex / modification-dependent protein catabolic process / ubiquitin-protein transferase activity / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / mitochondrion / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fakih, R. / Sauve, V. / Gehring, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the second phosphoubiquitin-binding site in parkin. Authors: Fakih, R. / Sauve, V. / Gehring, 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 | ![]() | 173.4 KB | Display | ![]() |
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PDB format | ![]() | 137.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.6 KB | Display | ![]() |
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Full document | ![]() | 471 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6glcS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 26406.189 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: S4X0T1, RBR-type E3 ubiquitin transferase |
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#2: Protein | Mass: 8542.706 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 50 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Bis-Tris propane pH 7.5, 20.5% PEG3350, 0.2M NaI |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1808 Å / Relative weight: 1 |
Reflection | Resolution: 2.484→47.59 Å / Num. obs: 19185 / % possible obs: 99.9 % / Redundancy: 18.3 % / CC1/2: 0.999 / Net I/σ(I): 21.08 |
Reflection shell | Resolution: 2.484→2.573 Å / Num. unique obs: 1847 / CC1/2: 0.523 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6GLC Resolution: 2.484→47.59 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.25 Å2 / Biso mean: 77.6442 Å2 / Biso min: 41.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.484→47.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -25.6556 Å / Origin y: 31.6822 Å / Origin z: -21.745 Å
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Refinement TLS group |
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