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Yorodumi- PDB-2d6m: Crystal structure of mouse galectin-9 N-terminal CRD in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d6m | |||||||||
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Title | Crystal structure of mouse galectin-9 N-terminal CRD in complex with lactose | |||||||||
Components | lectin, galactose binding, soluble 9 | |||||||||
Keywords | SUGAR BINDING PROTEIN / beta sandwich / carbohydrate binding protein / galectin / Structural Genomics | |||||||||
Function / homology | Function and homology information 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 interleukin-10 production / positive regulation of SMAD protein signal transduction / 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 | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Nagae, M. / Nishi, N. / Nakamura, T. / Wakatsuki, S. / Kato, R. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d6m.cif.gz | 93.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d6m.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d6m_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2d6m_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2d6m_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 2d6m_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/2d6m ftp://data.pdbj.org/pub/pdb/validation_reports/d6/2d6m | HTTPS FTP |
-Related structure data
Related structure data | 2d6kC 2d6lC 2d6nC 2d6oC 2d6pC 1a3kS 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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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.) Mus musculus (house mouse) / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99L83, UniProt: O08573*PLUS #2: Polysaccharide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 5% PEG6000, 0.1M citrate (pH5.0), VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.978 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 38497 / % possible obs: 93.7 % / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.345 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1A3K Resolution: 1.6→49.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.198 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.114 / 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: 16.102 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→49.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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