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Open data
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Basic information
Entry | Database: PDB / ID: 2xn4 | ||||||
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Title | Crystal structure of the kelch domain of human KLHL2 (Mayven) | ||||||
![]() | KELCH-LIKE PROTEIN 2 | ||||||
![]() | STRUCTURAL PROTEIN / CYTOSKELETON | ||||||
Function / homology | ![]() Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ruffle / Antigen processing: Ubiquitination & Proteasome degradation / actin cytoskeleton / lamellipodium / Neddylation / actin binding / protein ubiquitination / identical protein binding ...Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ruffle / Antigen processing: Ubiquitination & Proteasome degradation / actin cytoskeleton / lamellipodium / Neddylation / actin binding / protein ubiquitination / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Canning, P. / Hozjan, V. / Cooper, C.D.O. / Ayinampudi, V. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Canning, P. / Hozjan, V. / Cooper, C.D.O. / Ayinampudi, V. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. | ||||||
![]() | ![]() Title: Structural Basis for Cul3 Assembly with the Btb-Kelch Family of E3 Ubiquitin Ligases. Authors: Canning, P. / Cooper, C.D.O. / Krojer, T. / Murray, J.W. / Pike, A.C.W. / Chaikuad, A. / Keates, T. / Thangaratnarajah, C. / Hojzan, V. / Marsden, B.D. / Gileadi, O. / Knapp, S. / von Delft, F. / 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 | ![]() | 231.7 KB | Display | ![]() |
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PDB format | ![]() | 183.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
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Full document | ![]() | 452.3 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vpjC ![]() 3ii7C ![]() 4ap2C ![]() 4apfC ![]() 4ascC ![]() 3adeS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 306 - 591 / Label seq-ID: 15 - 300
NCS oper: (Code: given Matrix: (-0.36691, -0.93026, -0.00029), Vector: |
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Components
#1: Protein | Mass: 32830.262 Da / Num. of mol.: 2 / Fragment: KELCH DOMAIN, RESIDUES 294-591 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.59 % / Description: NONE |
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Crystal grow | Details: 0.2M (NH4)2SO4, 0.1M MES PH 6.5, 30% PEG 5000 MME, 0.2M NASCN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: May 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→19.83 Å / Num. obs: 34329 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.99→2.09 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.3 / % possible all: 67.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ADE Resolution: 1.99→19.82 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.286 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 10.168 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→19.82 Å
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Refine LS restraints |
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