+Open data
-Basic information
Entry | Database: PDB / ID: 4zmw | ||||||
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Title | Crystal structure of human P-cadherin (enc-X-dimer) | ||||||
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 / Adherens junctions interactions / catenin complex ...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 / Adherens junctions interactions / catenin complex / 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 / positive regulation of canonical Wnt signaling pathway / 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: 2.3 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 | 4zmw.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zmw.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zmw_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 4zmw_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 4zmw_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4zmw_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/4zmw ftp://data.pdbj.org/pub/pdb/validation_reports/zm/4zmw | HTTPS FTP |
-Related structure data
Related structure data | 4zmlC 4zmnSC 4zmoC 4zmpC 4zmqC 4zmtC 4zmvC 4zmxC 4zmyC 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: 23407.039 Da / Num. of mol.: 2 / Fragment: UNP residues 108-320 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 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.15 M Lithium sulfate 7.5 mM nickel sulfate 100 mM TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.02 Å / Num. obs: 33629 / % possible obs: 98.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 4.8 / % possible all: 92 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZMN Resolution: 2.3→47.02 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.862 / SU B: 6.571 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.213 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.492 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→47.02 Å
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Refine LS restraints |
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