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Open data
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Basic information
Entry | Database: PDB / ID: 4k95 | ||||||
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Title | Crystal Structure of Parkin | ||||||
![]() | E3 ubiquitin-protein ligase parkin | ||||||
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Function / homology | ![]() Josephin domain DUBs / Aggrephagy / positive regulation of neurotransmitter uptake / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seirafi, M. / Menade, M. / Sauve, V. / Kozlov, G. / Trempe, J.-F. / Nagar, B. / Gehring, K. | ||||||
![]() | ![]() Title: Structure of parkin reveals mechanisms for ubiquitin ligase activation. Authors: Trempe, J.F. / Sauve, V. / Grenier, K. / Seirafi, M. / Tang, M.Y. / Menade, M. / Al-Abdul-Wahid, S. / Krett, J. / Wong, K. / Kozlov, G. / Nagar, B. / Fon, E.A. / 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 | ![]() | 778.1 KB | Display | ![]() |
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PDB format | ![]() | 621.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4k7dSC ![]() 2zeqS 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
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Components
#1: Protein | Mass: 52155.113 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: Codon-optimized for E.coli expression / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9JK66, ![]() #2: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.74 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 6.5→50 Å / Num. all: 14952 / Num. obs: 14922 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 227 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.574 / Net I/σ(I): 15.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72) Resolution: 6.499→49.334 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7121 / SU ML: 1.11 / σ(F): 1.34 / Phase error: 34.11 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 213.59 Å2 / Biso mean: 88.6785 Å2 / Biso min: 28.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.499→49.334 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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