+Open data
-Basic information
Entry | Database: PDB / ID: 3k5r | ||||||
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Title | Crystal Structure of mouse T-cadherin EC1 EC2 | ||||||
Components | Cadherin 13 | ||||||
Keywords | STRUCTURAL PROTEIN / cadherin / mouse | ||||||
Function / homology | Function and homology information low-density lipoprotein particle mediated signaling / adiponectin binding / regulation of epidermal growth factor receptor signaling pathway / : / Adherens junctions interactions / localization within membrane / cell-cell adhesion mediated by cadherin / low-density lipoprotein particle binding / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of cell adhesion ...low-density lipoprotein particle mediated signaling / adiponectin binding / regulation of epidermal growth factor receptor signaling pathway / : / Adherens junctions interactions / localization within membrane / cell-cell adhesion mediated by cadherin / low-density lipoprotein particle binding / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of cell adhesion / catenin complex / cell-cell junction assembly / adherens junction organization / sprouting angiogenesis / positive regulation of positive chemotaxis / lamellipodium assembly / positive regulation of cell-matrix adhesion / Rac protein signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / lipoprotein particle binding / Rho protein signal transduction / regulation of endocytosis / keratinocyte proliferation / endothelial cell migration / GABA-ergic synapse / positive regulation of calcium-mediated signaling / positive regulation of endothelial cell proliferation / caveola / adherens junction / positive regulation of smooth muscle cell proliferation / cell morphogenesis / positive regulation of cell migration / neuron projection / cadherin binding / negative regulation of cell population proliferation / external side of plasma membrane / synapse / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å | ||||||
Authors | Shapiro, L. / Ciatto, C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: T-cadherin structures reveal a novel adhesive binding mechanism Authors: Ciatto, C. / Bahna, F. / Zampieri, N. / Vansteenhouse, H.C. / Katsamba, P.S. / Ahlsen, G. / Harrison, O.J. / Brasch, J. / Jin, X. / Posy, S. / Vendome, J. / Ranscht, B. / Jessell, T.M. / Honig, B. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k5r.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k5r.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 3k5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/3k5r ftp://data.pdbj.org/pub/pdb/validation_reports/k5/3k5r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23900.697 Da / Num. of mol.: 2 / Fragment: Domain EC1 and EC2 (UNP residues 140 to 355) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDK4, UniProt: Q9WTR5*PLUS #2: 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: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 50% saturated ammonium sulfate, 33mM Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 34355 / Num. obs: 34355 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.67 |
Reflection shell | Highest resolution: 2 Å / Rmerge(I) obs: 0.273 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.359 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.1 Å2 / Biso mean: 29.651 Å2 / Biso min: 13.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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