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- PDB-5un2: Crystal Structure of Mouse Cadherin-23 EC19-21 with non-syndromic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5un2 | |||||||||
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Title | Crystal Structure of Mouse Cadherin-23 EC19-21 with non-syndromic deafness (DFNB12) associated mutation R2029W | |||||||||
![]() | Cadherin-23 | |||||||||
![]() | CELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein | |||||||||
Function / homology | ![]() cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance / catenin complex / auditory receptor cell stereocilium organization / inner ear morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Jaiganesh, A. / Sotomayor, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness. Authors: Jaiganesh, A. / De-la-Torre, P. / Patel, A.A. / Termine, D.J. / Velez-Cortes, F. / Chen, C. / Sotomayor, 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 | ![]() | 149.8 KB | Display | ![]() |
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PDB format | ![]() | 115.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.1 KB | Display | ![]() |
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Full document | ![]() | 421.6 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i8dC ![]() 5tfkSC ![]() 5tflC ![]() 5tfmC ![]() 5uluC ![]() 5uz8C ![]() 5vh2C ![]() 5vt8C ![]() 5vvmC ![]() 5w4tC ![]() 5wj8C ![]() 5wjmC 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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Unit cell |
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Components on special symmetry positions |
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Details | Monomer as determined by Size exclusion chromatography |
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Components
#1: Protein | Mass: 37578.770 Da / Num. of mol.: 1 / Fragment: residues 1955-2289 / Mutation: R2029W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.64 Å3/Da / Density % sol: 73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.1 M HEPES pH 7.3 0.1 M CaCl2 27% PEG 400 5% glycerol PH range: 7.1-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→50 Å / Num. obs: 14294 / % possible obs: 91.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.087 / Rrim(I) all: 0.187 / Χ2: 1.013 / Net I/σ(I): 7.863 |
Reflection shell | Resolution: 2.96→3.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 667 / Rpim(I) all: 0.294 / Rrim(I) all: 0.631 / Χ2: 1.025 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TFK Resolution: 2.96→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.905 / SU B: 26.728 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.729 / ESU R Free: 0.338 / 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: 48.334 Å2
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Refinement step | Cycle: 1 / Resolution: 2.96→50 Å
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Refine LS restraints |
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