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- PDB-5lnp: Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lnp | ||||||
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Title | Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from monomeric fraction | ||||||
![]() | (Segment polarity protein dishevelled homolog DVL-2) x 2 | ||||||
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Function / homology | ![]() Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle ...Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Renko, M. / Gammons, M.V. / Bienz, M. | ||||||
![]() | ![]() Title: Wnt Signalosome Assembly by DEP Domain Swapping of Dishevelled. Authors: Gammons, M.V. / Renko, M. / Johnson, C.M. / Rutherford, T.J. / Bienz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.8 KB | Display | ![]() |
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PDB format | ![]() | 128 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 10862.361 Da / Num. of mol.: 3 / Fragment: DEP domain, UNP residues 416-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | | Mass: 10846.361 Da / Num. of mol.: 1 / Fragment: DEP domain, UNP residues 416-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.88 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES, pH=6.5 0.1 M NaCl 0.1 M Li2SO4 23 % PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.99→42.02 Å / Num. obs: 29398 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.3 | |||||||||||||||
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2884 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: unpublished model Resolution: 1.99→42.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.387 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.035 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.899 Å2
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Refinement step | Cycle: 1 / Resolution: 1.99→42.02 Å
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Refine LS restraints |
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