+Open data
-Basic information
Entry | Database: PDB / ID: 5kj4 | ||||||
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Title | Crystal Structure of Mouse Protocadherin-15 EC9-10 | ||||||
Components | Protocadherin-15 | ||||||
Keywords | Calcium-binding protein / hearing / mechanotransduction / adhesion | ||||||
Function / homology | Function and homology information 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 / auditory receptor cell stereocilium organization / adult walking behavior / 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 / auditory receptor cell stereocilium organization / adult walking behavior / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / visual perception / locomotory behavior / actin filament organization / morphogenesis of an epithelium / 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | ||||||
Authors | Araya-Secchi, R. / Sotomayor, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2016 Title: An elastic element in the protocadherin-15 tip link of the inner ear. Authors: Araya-Secchi, R. / Neel, B.L. / Sotomayor, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kj4.cif.gz | 361.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kj4.ent.gz | 297.9 KB | Display | PDB format |
PDBx/mmJSON format | 5kj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/5kj4 ftp://data.pdbj.org/pub/pdb/validation_reports/kj/5kj4 | HTTPS FTP |
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-Related structure data
Related structure data | 4xhzSC 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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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 25971.160 Da / Num. of mol.: 4 / Fragment: Cadherin 9 and 10, residues 924-1149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21 / References: UniProt: Q99PJ1 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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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: 5.71 Å3/Da / Density % sol: 78.47 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.095M HEPES (pH7.5), 0.19M CaCl2, 26.6% v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: oxford cryo-jet crystal cryocoolers | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2015 | |||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.35→50 Å / Num. obs: 31590 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 69.9 Å2 / CC1/2: 0.91 / Rmerge(I) obs: 0.256 / Net I/σ(I): 6.96 | |||||||||||||||||||||||||
Reflection shell | Resolution: 3.35→3.41 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 2.03 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XHZ Resolution: 3.35→46.98 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / SU B: 16.758 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.068 / 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: 77.308 Å2
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Refinement step | Cycle: LAST / Resolution: 3.35→46.98 Å
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Refine LS restraints |
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