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Open data
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Basic information
Entry | Database: PDB / ID: 8cia | ||||||
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Title | Crystal structure of the kelch domain of human KLHL20 | ||||||
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![]() | LIGASE / Kelch / E3 Ligase / KLHL20 | ||||||
Function / homology | ![]() type II interferon binding / protein K33-linked ubiquitination / response to interferon-alpha / Golgi to endosome transport / Cul3-RING ubiquitin ligase complex / cytoskeleton organization / trans-Golgi network / PML body / ubiquitin-protein transferase activity / protein transport ...type II interferon binding / protein K33-linked ubiquitination / response to interferon-alpha / Golgi to endosome transport / Cul3-RING ubiquitin ligase complex / cytoskeleton organization / trans-Golgi network / PML body / ubiquitin-protein transferase activity / protein transport / Antigen processing: Ubiquitination & Proteasome degradation / actin cytoskeleton / Neddylation / actin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / axon / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sweeney, M.N. / Bradshaw, W.J. / Chen, Z. / Bullock, A.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the kelch domain of human KLHL20 Authors: Sweeney, M.N. / Bradshaw, W.J. / Chen, Z. / Bullock, A.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.5 KB | Display | ![]() |
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PDB format | ![]() | 220.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.4 KB | Display | ![]() |
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Full document | ![]() | 496.1 KB | Display | |
Data in XML | ![]() | 51.6 KB | Display | |
Data in CIF | ![]() | 69.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33321.414 Da / Num. of mol.: 3 / Mutation: C316A, C327A, C402A, C426A, C604A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 33321.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | | Mass: 33322.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20% PEG2000MME, 0.2M Trimethylamine N-Oxide, 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.72→132.44 Å / Num. obs: 27259 / % possible obs: 95.8 % / Redundancy: 20.4 % / Biso Wilson estimate: 79.84 Å2 / CC1/2: 1 / Net I/σ(I): 8 |
Reflection shell | Resolution: 3.72→3.78 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1405 / CC1/2: 0.6 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 85.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.72→71.23 Å
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Refine LS restraints |
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LS refinement shell |
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