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Yorodumi- PDB-6rhm: Room temperature data of Galectin-3C in complex with a pair of en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rhm | ||||||
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Title | Room temperature data of Galectin-3C in complex with a pair of enantiomeric ligands: S enantiomer | ||||||
Components | Galectin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE-BINDING PROTEIN / GALACTOSE-SPECIFIC LECTIN 3 / GALACTOSIDE-BINDING PROTEIN / GALBP / IGE-6 BINDING PROTEIN / L-31 / LAMININ-BINDING PROTEIN / LECTIN L-29 / MAC-2 | ||||||
Function / homology | Function and homology information negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / 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 / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / 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 / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / 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 / positive chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / macrophage chemotaxis / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / RNA splicing / 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 / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.596 Å | ||||||
Authors | Kumar, R. / Verteramo, M.L. / Nilsson, U.J. / Logan, D.T. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Phys Chem Chem Phys / Year: 2019 Title: Are crystallographic B-factors suitable for calculating protein conformational entropy? Authors: Caldararu, O. / Kumar, R. / Oksanen, E. / Logan, D.T. / Ryde, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rhm.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rhm.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/6rhm ftp://data.pdbj.org/pub/pdb/validation_reports/rh/6rhm | HTTPS FTP |
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-Related structure data
Related structure data | 6rhlC 3zslS S: Starting model for refinement C: citing same article (ref.) |
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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: 15701.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17931 |
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#2: Chemical | ChemComp-J1E / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 4000, 0.1 M Tris/HCl pH 7.5, 0.4 M NaSCN, 7.9 mM beta-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.652 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.652 Å / Relative weight: 1 |
Reflection | Resolution: 1.596→31.91 Å / Num. obs: 19001 / % possible obs: 99.66 % / Redundancy: 8.7 % / Biso Wilson estimate: 20.54 Å2 / Rmerge(I) obs: 0.1642 / Net I/σ(I): 6.65 |
Reflection shell | Resolution: 1.596→1.653 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.9832 / Num. unique obs: 1853 / CC1/2: 0.438 / % possible all: 98.61 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3ZSL Resolution: 1.596→31.91 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.596→31.91 Å
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Refine LS restraints |
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LS refinement shell |
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