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- PDB-2d6p: Crystal structure of mouse galectin-9 N-terminal CRD in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2d6p | |||||||||
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Title | Crystal structure of mouse galectin-9 N-terminal CRD in complex with T-antigen | |||||||||
![]() | lectin, galactose binding, soluble 9 | |||||||||
![]() | SUGAR BINDING PROTEIN / beta sandwich / carbohydrate binding protein / galectin / Structural Genomics | |||||||||
Function / homology | ![]() regulation of natural killer cell differentiation / negative regulation of natural killer cell degranulation / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / positive regulation of oxidoreductase activity / maintenance of protein location / positive regulation of interleukin-1 production / galactoside binding / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation ...regulation of natural killer cell differentiation / negative regulation of natural killer cell degranulation / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / positive regulation of oxidoreductase activity / maintenance of protein location / positive regulation of interleukin-1 production / galactoside binding / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / positive regulation of innate immune response / positive regulation of macrophage activation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / immune system process / receptor clustering / positive regulation of SMAD protein signal transduction / positive regulation of interleukin-10 production / negative regulation of type II interferon production / positive regulation of T cell migration / positive regulation of chemokine production / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / positive regulation of cytokine production / female pregnancy / cellular response to virus / negative regulation of inflammatory response / chemotaxis / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / carbohydrate binding / collagen-containing extracellular matrix / response to lipopolysaccharide / negative regulation of gene expression / signaling receptor binding / positive regulation of gene expression / enzyme binding / extracellular region / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nagae, M. / Nishi, N. / Nakamura, T. / Murata, T. / Wakatsuki, S. / Kato, R. | |||||||||
![]() | ![]() Title: Crystal Structure of the Galectin-9 N-terminal Carbohydrate Recognition Domain from Mus musculus Reveals the Basic Mechanism of Carbohydrate Recognition Authors: Nagae, M. / Nishi, N. / Murata, T. / Usui, T. / Nakamura, T. / Wakatsuki, S. / Kato, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2d6kC ![]() 2d6lC ![]() 2d6mC ![]() 2d6nC ![]() 2d6oC ![]() 1a3kS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 18169.768 Da / Num. of mol.: 2 Fragment: N-terminal carbohydrate recognition domain(RESIDUES 1-157) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.32 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 15% ethanol, 0.1M CHES (pH9.5) , VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 11336 / % possible obs: 100 % / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.307 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1A3K Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.828 / SU B: 13.254 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 1.087 / ESU R Free: 0.389 / 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: 28.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.697→2.767 Å / Total num. of bins used: 20
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