+Open data
-Basic information
Entry | Database: PDB / ID: 3k6d | ||||||
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Title | Crystal structure of Xenopus laevis T-cadherin EC1 | ||||||
Components | T-cadherin | ||||||
Keywords | CELL ADHESION / T-cadherin | ||||||
Function / homology | Function and homology information : / homophilic cell adhesion via plasma membrane adhesion molecules / calcium ion binding / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 | 3k6d.cif.gz | 33.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k6d.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 3k6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/3k6d ftp://data.pdbj.org/pub/pdb/validation_reports/k6/3k6d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10797.280 Da / Num. of mol.: 1 / Fragment: EC1 domain: UNP residues 136-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: cdh13, LOC495024 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XHE3 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50mM Zn acetate, 20 % PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD Details: Horizontal focusing sagitally bent second mono crystal |
Radiation | Monochromator: Cryogenically cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 17500 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 24.52 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→27.902 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.787 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 68.29 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.01 Å2 / Biso mean: 31.143 Å2 / Biso min: 3.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.902 Å
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Refine LS restraints |
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LS refinement shell |
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