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Open data
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Basic information
Entry | Database: PDB / ID: 5caw | |||||||||
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Title | Structure of Pediculus humanus Parkin bound to phospho-ubiquitin | |||||||||
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![]() | SIGNALING PROTEIN / ubiquitin / Parkin / PINK1 / phospho-ubiquitin / Parkinson's disease / E3 ligase / RBR domain / mitophagy / cell signalling | |||||||||
Function / homology | ![]() positive regulation of metabolic process / RBR-type E3 ubiquitin transferase / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / autophagy / ubiquitin-protein transferase activity / protein ubiquitination / mitochondrion / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wauer, T. / Komander, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of phospho-ubiquitin-induced PARKIN activation. Authors: Wauer, T. / Simicek, M. / Schubert, A. / Komander, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.3 KB | Display | ![]() |
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PDB format | ![]() | 243.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.8 KB | Display | ![]() |
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Full document | ![]() | 480.8 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 41.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5c9vC ![]() 1ubqS ![]() 4bm9S 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: 36100.445 Da / Num. of mol.: 2 / Fragment: UNP residues 141-461 Source method: isolated from a genetically manipulated source Details: covalently modified with phospho-ubiquitin at Cys349 Source: (gene. exp.) ![]() Gene: Phum_PHUM233570 / Plasmid: pOKINK / Production host: ![]() ![]() References: UniProt: E0VIU9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein | Mass: 8640.854 Da / Num. of mol.: 2 / Mutation: G76 exchanged to chemical probe Source method: isolated from a genetically manipulated source Details: phosphorylated at Ser65 Gly76 exchanged with chemical probe, bromopropylamine. The bromide was lost during the coupling. Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→34.06 Å / Num. obs: 26558 / % possible obs: 99.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.62→2.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4bm9, 1ubq Resolution: 2.62→34.055 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→34.055 Å
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Refine LS restraints |
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LS refinement shell |
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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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