+Open data
-Basic information
Entry | Database: PDB / ID: 4zmy | ||||||
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Title | Crystal structure of human P-cadherin (monomer 1) | ||||||
Components | Cadherin-3 | ||||||
Keywords | CELL ADHESION / dimerization / conformational change | ||||||
Function / homology | Function and homology information negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / Adherens junctions interactions ...negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / Adherens junctions interactions / retina homeostasis / cell-cell junction assembly / adherens junction organization / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell adhesion via plasma membrane adhesion molecules / visual perception / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / cell morphogenesis / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / cell migration / cell junction / cell adhesion / response to xenobiotic stimulus / cadherin binding / calcium ion binding / positive regulation of gene expression / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Caaveiro, J.M.M. / Kudo, S. / Tsumoto, K. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism Authors: Kudo, S. / Caaveiro, J.M. / Tsumoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zmy.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zmy.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/4zmy ftp://data.pdbj.org/pub/pdb/validation_reports/zm/4zmy | HTTPS FTP |
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-Related structure data
Related structure data | 4zmlC 4zmnSC 4zmoC 4zmpC 4zmqC 4zmtC 4zmvC 4zmwC 4zmxC 4zmzC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23421.945 Da / Num. of mol.: 1 / Fragment: UNP residues 108-320 / Mutation: K14E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3, CDHP / Plasmid: Champion pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22223 | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 4,000 100 mM CaCl2 100 mM TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→26.22 Å / Num. obs: 32358 / % possible obs: 91.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.2 / % possible all: 64.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZMN Resolution: 1.5→26.22 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.217 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.075 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.136 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→26.22 Å
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Refine LS restraints |
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