+Open data
-Basic information
Entry | Database: PDB / ID: 5wj8 | |||||||||
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Title | Crystal Structure of Human Cadherin-23 EC13-14 | |||||||||
Components | Cadherin-23 | |||||||||
Keywords | CELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN | |||||||||
Function / homology | Function and homology information kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / 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 ...kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / 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 / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of cytosolic calcium ion concentration / visual perception / photoreceptor inner segment / locomotory behavior / sensory perception of sound / beta-catenin binding / calcium ion transport / neuron projection development / cell migration / cadherin binding / centrosome / calcium ion binding / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | |||||||||
Authors | Velez-Cortes, F. / Conghui, C. / 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 | 5wj8.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wj8.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/5wj8 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/5wj8 | HTTPS FTP |
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-Related structure data
Related structure data | 5i8dC 5tfkC 5tflC 5tfmC 5uluC 5un2C 5uz8C 5vh2SC 5vt8C 5vvmC 5w4tC 5wjmC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24742.354 Da / Num. of mol.: 1 / Fragment: residues 1308-1523 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDH23, KIAA1774, KIAA1812, UNQ1894/PRO4340 / Plasmid: pET21a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-RIPL / References: UniProt: Q9H251 | ||||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-K / | #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: 3.48 Å3/Da / Density % sol: 64.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M NaOAc pH 4.5 0.2 M CaCl2 30 (v/v) isopropanol 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→71.17 Å / Num. obs: 30738 / % possible obs: 94.4 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2 / Num. unique obs: 1246 / % possible all: 83.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VH2 Resolution: 1.86→71.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.581 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / 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: 45.936 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→71.17 Å
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Refine LS restraints |
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