+Open data
-Basic information
Entry | Database: PDB / ID: 5i8d | ||||||
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Title | Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P | ||||||
Components | Cadherin-23 | ||||||
Keywords | CELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein | ||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Jaiganesh, A. / Sotomayor, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i8d.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i8d.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 5i8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/5i8d ftp://data.pdbj.org/pub/pdb/validation_reports/i8/5i8d | HTTPS FTP |
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-Related structure data
Related structure data | 5tfkC 5tflC 5tfmC 5uluC 5un2C 5uz8C 5vh2C 5vt8C 5vvmC 5w4tC 5wj8C 5wjmC 2a62S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38217.414 Da / Num. of mol.: 1 / Mutation: S2087P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET-21 a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: Q99PF4 | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 0.025M Calcium Acetate, 0.1 M Sodium Cacodylate, 25% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford Cryo-Jet crystal cryocoolers |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→111.36 Å / Num. obs: 15826 / % possible obs: 98.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.38 |
Reflection shell | Resolution: 2.69→2.75 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Cadherin-8 (2A62) Resolution: 2.69→111.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 36.516 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.289 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.301 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→111.36 Å
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Refine LS restraints |
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