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Open data
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Basic information
Entry | Database: PDB / ID: 6bxu | |||||||||
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Title | Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T | |||||||||
![]() | Protocadherin-15 | |||||||||
![]() | CELL ADHESION / Hearing / Mechanotransduction / Adhesion / Calcium-binding protein | |||||||||
Function / homology | ![]() detection of mechanical stimulus involved in equilibrioception / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / adult walking behavior / auditory receptor cell stereocilium organization / startle response ...detection of mechanical stimulus involved in equilibrioception / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / adult walking behavior / auditory receptor cell stereocilium organization / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / visual perception / locomotory behavior / morphogenesis of an epithelium / actin filament organization / sensory perception of sound / multicellular organism growth / response to calcium ion / cell adhesion / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Neel, B.L. / Sotomayor, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception. Authors: Choudhary, D. / Narui, Y. / Neel, B.L. / Wimalasena, L.N. / Klanseck, C.F. / De-la-Torre, P. / Chen, C. / Araya-Secchi, R. / Tamilselvan, E. / Sotomayor, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.1 KB | Display | ![]() |
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PDB format | ![]() | 212 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.9 KB | Display | ![]() |
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Full document | ![]() | 437.9 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tpkC ![]() 5ulyC ![]() 5w1dSC ![]() 6bwnC ![]() 6e8fC ![]() 6eb5C ![]() 6eetC ![]() 6mfoC ![]() 6n22C ![]() 6n2eC S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 35208.910 Da / Num. of mol.: 2 / Fragment: CADHERIN DOMAINS 5-7, RESIDUES 507-818 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.66 Å3/Da / Density % sol: 83.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Na formate, 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 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: 3.79→180.9 Å / Num. obs: 21629 / % possible obs: 97.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.231 / Net I/σ(I): 7.43 |
Reflection shell | Resolution: 3.79→3.87 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 0.545 / Num. unique obs: 946 / CC1/2: 0.269 / % possible all: 87.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5W1D Resolution: 3.79→180.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 76.706 / SU ML: 0.465 / Cross valid method: THROUGHOUT / ESU R: 2.039 / ESU R Free: 0.537 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 150.424 Å2
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Refinement step | Cycle: 1 / Resolution: 3.79→180.9 Å
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Refine LS restraints |
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