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- PDB-2whv: CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 (ALL CATION BINDING ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2whv | ||||||
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Title | CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 (ALL CATION BINDING SITES OCCUPIED BY CALCIUM) | ||||||
![]() | CADHERIN-23 | ||||||
![]() | CELL ADHESION / HEARING / DEAFNESS | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P. | ||||||
![]() | ![]() Title: Structural Determinants of Cadherin-23 Function in Hearing and Deafness. Authors: Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.9 KB | Display | ![]() |
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PDB format | ![]() | 47.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 432.4 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wbxC ![]() 2wcpSC ![]() 2wd0C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23856.436 Da / Num. of mol.: 1 / Fragment: EC1-2, RESIDUES 24-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 197 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-TERMINAL METHIONINE IS A CLONING ARTIFACT. PROTEIN WAS CLONED WITH AN ADDITIONAL C-TERMINAL HIS- ...N-TERMINAL METHIONINE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.28 Å3/Da / Density % sol: 80.43 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M MES PH 6.5, 1.1 M CALCIUM CHLORIDE DIHYDRATE, 0.15 M POTASSIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 3, 2009 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→22.25 Å / Num. obs: 24907 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.65 |
Reflection shell | Resolution: 2.36→2.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WCP Resolution: 2.36→22.25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.801 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL CADHERIN CATION BINDING SITES ARE OCCUPIED BY CALCIUM
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.743 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→22.25 Å
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Refine LS restraints |
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