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Open data
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Basic information
Entry | Database: PDB / ID: 5vvm | |||||||||
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Title | Crystal structure of human CDH23 EC21-23 | |||||||||
![]() | Cadherin-23![]() | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() cochlear hair cell ribbon synapse / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Patel, A. / Jaiganesh, A. / Sotomayor, M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 250.7 KB | Display | ![]() |
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PDB format | ![]() | 201.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5i8dSC ![]() 5tfkC ![]() 5tflC ![]() 5tfmC ![]() 5uluC ![]() 5un2C ![]() 5uz8SC ![]() 5vh2C ![]() 5vt8C ![]() 5w4tC ![]() 5wj8C ![]() 5wjmC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 2153 - 2473 / Label seq-ID: 9 - 329
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Components
#1: Protein | ![]() Mass: 37892.051 Da / Num. of mol.: 2 / Fragment: residues 2169-2505 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: 3.01 Å3/Da / Density % sol: 59.07 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.05 M TRIS pH 8.5 0.5 M NaCl 10% PEG-4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.54→94.08 Å / Num. obs: 10856 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.95 |
Reflection shell | Resolution: 3.54→3.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5I8D, 5UZ8 Resolution: 3.54→94.08 Å / Cor.coef. Fo:Fc: 0.804 / Cor.coef. Fo:Fc free: 0.727 / SU B: 109.744 / SU ML: 0.7 / Cross valid method: THROUGHOUT / ESU R Free: 0.851 / 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: 66.92 Å2
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Refinement step | Cycle: LAST / Resolution: 3.54→94.08 Å
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Refine LS restraints |
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