+Open data
-Basic information
Entry | Database: PDB / ID: 5wjm | |||||||||
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Title | Crystal Structure of Mouse Cadherin-23 EC17-18 | |||||||||
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: 2.9 Å | |||||||||
Authors | De-la-Torre, P. / 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 | 5wjm.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wjm.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wjm_validation.pdf.gz | 430.6 KB | Display | wwPDB validaton report |
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Full document | 5wjm_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 5wjm_validation.xml.gz | 10 KB | Display | |
Data in CIF | 5wjm_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/5wjm ftp://data.pdbj.org/pub/pdb/validation_reports/wj/5wjm | HTTPS FTP |
-Related structure data
Related structure data | 5i8dC 5tfkC 5tflC 5tfmC 5uluC 5un2C 5uz8C 5vh2C 5vt8C 5vvmC 5w4tC 5wj8C 2wd0S 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: 25092.018 Da / Num. of mol.: 1 / Fragment: residues 1739-1954 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET21a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIPL / References: UniProt: Q99PF4 | ||||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-K / | #4: Chemical | #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: 3.26 Å3/Da / Density % sol: 62.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 0.1 M NaOAc pH 5.2 0.01 M MgCl2 25 % (v/v) MPD 25 mM 18-Crown-6 0.07 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Jul 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→86.6 Å / Num. obs: 7803 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.245 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 366 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wd0 Resolution: 2.9→86.6 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.844 / SU B: 16.147 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 1.202 / ESU R Free: 0.381 / 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: 27.858 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→86.6 Å
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