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Yorodumi- PDB-2wd0: CRYSTAL STRUCTURE OF NONSYNDROMIC DEAFNESS (DFNB12) ASSOCIATED MU... -
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Open data
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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 informationequilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / inner ear auditory receptor cell differentiation / calcium-dependent cell-cell adhesion / stereocilium ...equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / inner ear auditory receptor cell differentiation / calcium-dependent cell-cell adhesion / stereocilium / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / inner ear morphogenesis / homophilic cell-cell adhesion / inner ear development / cochlea development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / cell adhesion / calcium ion binding / synapse / centrosome / plasma membrane Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| 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: 2010Title: Structural Determinants of Cadherin-23 Function in Hearing and Deafness. Authors: Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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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 ( S: Starting model for refinement |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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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: 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.) ![]() ![]() #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 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting 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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