+Open data
-Basic information
Entry | Database: PDB / ID: 8tri | ||||||
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Title | Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A | ||||||
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 / inner ear receptor cell stereocilium organization / stereocilium tip / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / inner ear receptor cell stereocilium organization / stereocilium tip / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / stereocilium / 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 / beta-catenin binding / calcium ion transport / neuron projection development / cell migration / apical part of cell / cell adhesion / cadherin binding / centrosome / calcium ion binding / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.716 Å | ||||||
Authors | Ashraf, Q. / Sotomayor, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A Authors: Ashraf, Q. / Sotomayor, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tri.cif.gz | 289 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tri.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8tri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tri_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8tri_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8tri_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 8tri_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/8tri ftp://data.pdbj.org/pub/pdb/validation_reports/tr/8tri | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 53237.551 Da / Num. of mol.: 3 / Fragment: residues 2603-3065 / Mutation: F2894A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q99PF4 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.96 Å3/Da / Density % sol: 82.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 1.25 M Lithium Acetate, 0.1 M MES pH 7.2, 25% glycerol (cryo) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→50 Å / Num. obs: 47174 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.981 / CC star: 0.995 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3.7→3.76 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 2309 / CC1/2: 0.56 / CC star: 0.847 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.716→49.563 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.187 / SU B: 22.316 / SU ML: 0.306 / Average fsc free: 0.9625 / Average fsc work: 0.9768 / Cross valid method: FREE R-VALUE / ESU R: 1.416 / ESU R Free: 0.422 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 124.855 Å2
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Refinement step | Cycle: LAST / Resolution: 3.716→49.563 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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