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Yorodumi- PDB-6y4c: Structure of galectin-3C in complex with lactose determined by se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y4c | |||||||||
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Title | Structure of galectin-3C in complex with lactose determined by serial crystallography using an XtalTool support | |||||||||
Components | Galectin-3 | |||||||||
Keywords | SUGAR BINDING PROTEIN / galectin / synchrotron serial crystallography / solid support / XtalTool | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Shilova, A. / Hakansson, M. / Welin, M. / Kovacic, R. / Mueller, U. / Logan, D.T. | |||||||||
Funding support | Sweden, 1items
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Citation | Journal: J.Synchrotron Radiat. / Year: 2020 Title: Current status and future opportunities for serial crystallography at MAX IV Laboratory. Authors: Shilova, A. / Lebrette, H. / Aurelius, O. / Nan, J. / Welin, M. / Kovacic, R. / Ghosh, S. / Safari, C. / Friel, R.J. / Milas, M. / Matej, Z. / Hogbom, M. / Branden, G. / Kloos, M. / Shoeman, ...Authors: Shilova, A. / Lebrette, H. / Aurelius, O. / Nan, J. / Welin, M. / Kovacic, R. / Ghosh, S. / Safari, C. / Friel, R.J. / Milas, M. / Matej, Z. / Hogbom, M. / Branden, G. / Kloos, M. / Shoeman, R.L. / Doak, B. / Ursby, T. / Hakansson, M. / Logan, D.T. / Mueller, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y4c.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y4c.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 6y4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/6y4c ftp://data.pdbj.org/pub/pdb/validation_reports/y4/6y4c | HTTPS FTP |
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-Related structure data
Related structure data | 6y2nC 6y78C 6eymS 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 (E. coli) / References: UniProt: P17931 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 15555 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystals were grown on an XtalTool support (Jena Bioscience) over a 24 well VDX-plate with 1 ml reservoir. The drop consisted of 1 microlitre 20 mg/ml protein in 10 mM sodium phosphate pH 7. ...Details: Crystals were grown on an XtalTool support (Jena Bioscience) over a 24 well VDX-plate with 1 ml reservoir. The drop consisted of 1 microlitre 20 mg/ml protein in 10 mM sodium phosphate pH 7.4, 100 mM NaCl, 10 mM beta-mercaptoethanol, 2 mM lactose), 0.25 microlitre of seed crystals in a stabilization solution containing 0.1 M Tris pH 7.5, 33% (w/v) PEG 4000, 0.1 M MgCl2, 0.2 M NaSCN) and 0.75 microlitre reservoir solution containing 0.1 M Tris pH 7.5, 30% PEG 4000, 0.05 M MgCl2, 0.2 M NaSCN and 8 mM beta-mercaptoethanol. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→60 Å / Num. obs: 15552 / % possible obs: 99.9 % / Redundancy: 139 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.9589303 / R split: 0.141 / Net I/σ(I): 5.66 |
Reflection shell | Resolution: 1.7→1.75 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1660 / CC1/2: 0.7462656 / CC star: 0.86 / R split: 0.37 |
Serial crystallography measurement | Source size: 100 µm2 |
Serial crystallography sample delivery | Description: XtalTool (Jena Bioscience) / Method: fixed target |
Serial crystallography sample delivery fixed target | Description: Crystallized directly on XtalTool / Motion control: MD3 (Arinax) / Sample dehydration prevention: HCLab (Arinax) / Sample holding: SPINE pin |
Serial crystallography data reduction | Frame hits: 49446 / Frames failed index: 33891 / Frames indexed: 15555 / Frames total: 70537 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EYM Resolution: 1.7→42.91 Å / SU ML: 0.1526 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.1839 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→42.91 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.2007218783 Å / Origin y: 0.804730293698 Å / Origin z: 6.43951633506 Å
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Refinement TLS group | Selection details: ALL |