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Open data
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Basic information
Entry | Database: PDB / ID: 6iw3 | |||||||||
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Title | High resolution structure of Dvl2-DIX Y27W/C80S mutant | |||||||||
![]() | Segment polarity protein dishevelled homolog DVL-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 | ![]() ![]() ![]() | |||||||||
![]() | Yamanishi, K. / Shibata, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution structure of a Y27W mutant of the Dishevelled2 DIX domain. Authors: Yamanishi, K. / Sin, Y. / Terawaki, S.I. / Higuchi, Y. / Shibata, 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 | ![]() | 52.8 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wipS S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 9311.475 Da / Num. of mol.: 1 / Fragment: DIX-domain / Mutation: Y27W, C80S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% (w/v) PEG 6000, Tris-HCl pH 8.0, 200 mM lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.64→50 Å / Num. obs: 12127 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.136 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.64→1.68 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.3 / Num. unique obs: 873 / CC1/2: 0.511 / Rrim(I) all: 2.37 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4WIP Resolution: 1.64→38.5 Å / SU R Cruickshank DPI: 0.116 / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.64→38.5 Å
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LS refinement shell | Resolution: 1.64→1.702 Å
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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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