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Open data
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Basic information
Entry | Database: PDB / ID: 5nb8 | ||||||
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Title | Structure of vWC domain from CCN3 | ||||||
![]() | Protein NOV homolog | ||||||
![]() | SIGNALING PROTEIN / CCN3 / vWC / domains / signalling / BMP | ||||||
Function / homology | ![]() endothelial cell-cell adhesion / bone regeneration / smooth muscle cell proliferation / negative regulation of monocyte chemotaxis / negative regulation of chondrocyte proliferation / : / negative regulation of sensory perception of pain / hematopoietic stem cell homeostasis / negative regulation of myotube differentiation / endothelial cell chemotaxis ...endothelial cell-cell adhesion / bone regeneration / smooth muscle cell proliferation / negative regulation of monocyte chemotaxis / negative regulation of chondrocyte proliferation / : / negative regulation of sensory perception of pain / hematopoietic stem cell homeostasis / negative regulation of myotube differentiation / endothelial cell chemotaxis / fibroblast migration / type B pancreatic cell proliferation / gap junction / negative regulation of non-canonical NF-kappaB signal transduction / Notch binding / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of Notch signaling pathway / negative regulation of SMAD protein signal transduction / negative regulation of insulin secretion / chondrocyte differentiation / extracellular matrix / cell chemotaxis / growth factor activity / negative regulation of cell growth / negative regulation of inflammatory response / integrin binding / heparin binding / regulation of gene expression / angiogenesis / collagen-containing extracellular matrix / cell adhesion / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / signal transduction / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, E.-R. / Hyvonen, M. | ||||||
![]() | ![]() Title: Structural analyses of von Willebrand factor C domains of collagen 2A and CCN3 reveal an alternative mode of binding to bone morphogenetic protein-2. Authors: Xu, E.R. / Blythe, E.E. / Fischer, G. / Hyvonen, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.2 KB | Display | ![]() |
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PDB format | ![]() | 100.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10446.865 Da / Num. of mol.: 4 / Fragment: UNP residues 100-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-IMD / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.8 M Na/K Tartrate, 0.4M NaCl, 0.1 M Imidazole, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.58 Å / Num. obs: 25475 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.92 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3237 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→28.58 Å
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Refine LS restraints |
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LS refinement shell |
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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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