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- PDB-6fof: Crystal structure of a crystallized variant of h-Gal3: Gal-3[NTS/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fof | |||||||||
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Title | Crystal structure of a crystallized variant of h-Gal3: Gal-3[NTS/VII-IX] | |||||||||
![]() | Galectin-3,Galectin-3 | |||||||||
![]() | SUGAR BINDING PROTEIN / Galectin / apoptosis / glycosylation | |||||||||
Function / homology | ![]() negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / negative regulation of endocytosis / IgE binding / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / negative regulation of endocytosis / IgE binding / positive regulation of mononuclear cell migration / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / regulation of T cell proliferation / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / RNA splicing / neutrophil chemotaxis / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Romero, A. / Flores-Ibarra, A. / Medrano, F.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallization of a human galectin-3 variant with two ordered segments in the shortened N-terminal tail. Authors: Flores-Ibarra, A. / Vertesy, S. / Medrano, F.J. / Gabius, H.J. / Romero, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.4 KB | Display | ![]() |
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PDB format | ![]() | 291.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.6 MB | Display | ![]() |
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Full document | ![]() | 4.7 MB | Display | |
Data in XML | ![]() | 60.1 KB | Display | |
Data in CIF | ![]() | 82 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a3kS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21209.848 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18% PEG 8K, 100 mM Tris-HCl (pH 8.5), 200 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.1 Å / Num. obs: 112248 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 43.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rsym value: 0.142 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.233 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 16179 / CC1/2: 0.558 / Rsym value: 1.308 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A3K Resolution: 2.2→49.1 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||
Displacement parameters | Biso mean: 46.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.1 Å
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LS refinement shell | Resolution: 2.2→2.26 Å
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