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Yorodumi- PDB-2wd0: CRYSTAL STRUCTURE OF NONSYNDROMIC DEAFNESS (DFNB12) ASSOCIATED MU... -
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-Basic information
Entry | Database: PDB / ID: 2wd0 | ||||||
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Title | CRYSTAL STRUCTURE OF NONSYNDROMIC DEAFNESS (DFNB12) ASSOCIATED MUTANT D124G OF MOUSE CADHERIN-23 EC1-2 | ||||||
Components | CADHERIN-23 | ||||||
Keywords | CELL ADHESION / HEARING | ||||||
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: 2.74 Å | ||||||
Authors | Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P. | ||||||
Citation | Journal: Neuron / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wd0.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wd0.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wd0_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
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Full document | 2wd0_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 2wd0_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 2wd0_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wd0 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wd0 | HTTPS FTP |
-Related structure data
Related structure data | 2wbxC 2wcpSC 2whvC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 6
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 23798.400 Da / Num. of mol.: 2 / Fragment: EC1-2, RESIDUES 24-228 / Mutation: YES Source method: isolated from a genetically manipulated source Details: AMINO-ACID NUMBERING ACCORDING TO SEQUENCE OF CRYSTALLIZED CONSTRUCT. Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99PF4 #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | RESIDUE ASPARTATE 124 (DATABASE NUMBERING) IS MUTATED TO GLYCINE. | |
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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: 5.38 Å3/Da / Density % sol: 77.15 % / Description: NONE |
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Crystal grow | pH: 7.1 / Details: 0.1M SODIUM CACODYLATE PH 7.1, 1M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 28267 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.47 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WCP Resolution: 2.74→29.77 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.907 / SU B: 21.451 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT.
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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: SIMPLE SCALING | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.276 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→29.77 Å
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Refine LS restraints |
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