+Open data
-Basic information
Entry | Database: PDB / ID: 5uz8 | |||||||||
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Title | Crystal Structure of Mouse Cadherin-23 EC22-24 | |||||||||
Components | Cadherin-23 | |||||||||
Keywords | CELL ADHESION / Hearing / Mechanotransduction / Adhesion / Calcium-binding proteins | |||||||||
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 / photoreceptor ribbon synapse / cell-cell adhesion via plasma-membrane adhesion molecules / 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 / photoreceptor ribbon synapse / cell-cell adhesion via plasma-membrane adhesion molecules / 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: 1.85 Å | |||||||||
Authors | Patel, A. / Jaiganesh, A. / Sotomayor, M. | |||||||||
Funding support | United States, 2items
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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 | 5uz8.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uz8.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 5uz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/5uz8 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/5uz8 | HTTPS FTP |
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-Related structure data
Related structure data | 5i8dSC 5tfkC 5tflC 5tfmC 5uluC 5un2C 5vh2C 5vt8C 5vvmC 5w4tC 5wj8C 5wjmC C: citing same article (ref.) S: Starting model for refinement |
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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: 36533.301 Da / Num. of mol.: 1 / Fragment: residues 2288-2607 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET-21a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99PF4 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GSH / | #5: 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: 3.71 Å3/Da / Density % sol: 66.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 3.5 M Ammonium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 45949 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2224 / Χ2: 1.01 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I8D Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.704 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.095 / 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: 23.397 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→50 Å
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Refine LS restraints |
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