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Yorodumi- PDB-6exy: Neutron crystal structure of perdeuterated galectin-3C in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6exy | ||||||
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Title | Neutron crystal structure of perdeuterated galectin-3C in complex with glycerol | ||||||
Components | Galectin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / galectin / hydrogen bonding / molecular recognition / perdeuteration | ||||||
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 / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / FOURIER SYNTHESIS / Resolution: 1.1 Å | ||||||
Authors | Manzoni, F. / Schrader, T.E. / Ostermann, A. / Oksanen, E. / Logan, D.T. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J. Med. Chem. / Year: 2018 Title: Elucidation of Hydrogen Bonding Patterns in Ligand-Free, Lactose- and Glycerol-Bound Galectin-3C by Neutron Crystallography to Guide Drug Design. Authors: Manzoni, F. / Wallerstein, J. / Schrader, T.E. / Ostermann, A. / Coates, L. / Akke, M. / Blakeley, M.P. / Oksanen, E. / Logan, D.T. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C. Authors: Manzoni, F. / Saraboji, K. / Sprenger, J. / Kumar, R. / Noresson, A.L. / Nilsson, U.J. / Leffler, H. / Fisher, S.Z. / Schrader, T.E. / Ostermann, A. / Coates, L. / Blakeley, M.P. / Oksanen, E. / Logan, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6exy.cif.gz | 169.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6exy.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 6exy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/6exy ftp://data.pdbj.org/pub/pdb/validation_reports/ex/6exy | HTTPS FTP |
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-Related structure data
Related structure data | 6eymC 6f2qC 3zsjS 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: 15832.244 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: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 44 % / Description: Volume approximately 1.0 mm3 |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 12-15% PEG 4000 OR PEG 3000, 0.1M MGCL2, 0.015M BETA MERCAPTOETHANOL, 0.1M TRIS-DCL, PD 7.9, 0.4M NaSCN. All dissolved in D2O. Crystal grown in a 15 + 15 microlitre sitting drop that was ...Details: 12-15% PEG 4000 OR PEG 3000, 0.1M MGCL2, 0.015M BETA MERCAPTOETHANOL, 0.1M TRIS-DCL, PD 7.9, 0.4M NaSCN. All dissolved in D2O. Crystal grown in a 15 + 15 microlitre sitting drop that was first equilibrated for 1 week. A small crystal grown at 20-28% PEG was introduced. The drop was fed with fresh protein by adding 3-4 micro litres of protein with 10 mM lactose every 3-4 days for 3 months. Then the lactose was exchanged for glycerol by dialysis for at least one month against 10% glycerol (1.37 M), 24% PEG 4000 in the same buffer. For details see Manzoni et al. (2016). |
-Data collection
Diffraction |
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Radiation |
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Radiation wavelength |
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Reflection | Biso Wilson estimate: 11.45 Å2 / Entry-ID: 6EXY
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Reflection shell |
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-Processing
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Refinement | SU ML: 0.0845 / Cross valid method: FREE R-VALUE / Method to determine structure: FOURIER SYNTHESIS / Phase error: 14.161 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Starting model: 3ZSJ
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Refinement step | Cycle: LAST / Resolution: 1.1→31.93 Å
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Refine LS restraints |
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LS refinement shell |
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