+Open data
-Basic information
Entry | Database: PDB / ID: 7sgx | ||||||
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Title | Crystal Structure of Turtle Cadherin-23 EC1-2 | ||||||
Components | Cadherin 23 | ||||||
Keywords | CELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN | ||||||
Biological species | Chelonia mydas (Green sea turtle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å | ||||||
Authors | Nisler, C.R. / Sotomayor, M. | ||||||
Funding support | France, 1items
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Citation | Journal: Mol.Biol.Evol. / Year: 2023 Title: Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation. Authors: Nisler, C.R. / Narui, Y. / Scheib, E. / Choudhary, D. / Bowman, J.D. / Mandayam Bharathi, H. / Lynch, V.J. / Sotomayor, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sgx.cif.gz | 184.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sgx.ent.gz | 141.3 KB | Display | PDB format |
PDBx/mmJSON format | 7sgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sgx_validation.pdf.gz | 5.1 MB | Display | wwPDB validaton report |
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Full document | 7sgx_full_validation.pdf.gz | 5.2 MB | Display | |
Data in XML | 7sgx_validation.xml.gz | 31 KB | Display | |
Data in CIF | 7sgx_validation.cif.gz | 42.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/7sgx ftp://data.pdbj.org/pub/pdb/validation_reports/sg/7sgx | HTTPS FTP |
-Related structure data
Related structure data | 7n4pC 7sb6C 7scmC 8e51C 2whvS S: Starting model for refinement C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 24203.768 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: This sequence matches record XP_007054748.1 at NCBI: https://www.ncbi.nlm.nih.gov/protein/XP_007054748.1/?report=fasta Source: (gene. exp.) Chelonia mydas (Green sea turtle) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.18 Å3/Da / Density % sol: 70.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 0.1 M Tris pH 7.7 1.9 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.13→50 Å / Num. obs: 30114 / % possible obs: 99.8 % / Redundancy: 12.1 % / Rrim(I) all: 0.297 / Net I/σ(I): 12.559 |
Reflection shell | Resolution: 3.13→3.2 Å / Num. unique obs: 1456 / Rrim(I) all: 2.187 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WHV Resolution: 3.13→49.056 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.87 / SU B: 24.974 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / ESU R: 1.34 / ESU R Free: 0.474 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.691 Å2
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Refinement step | Cycle: LAST / Resolution: 3.13→49.056 Å
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Refine LS restraints |
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LS refinement shell |
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