+Open data
-Basic information
Entry | Database: PDB / ID: 4lbm | |||||||||
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Title | Crystal structure of Human galectin-3 CRD in complex with LNT | |||||||||
Components | Galectin-3 | |||||||||
Keywords | SUGAR BINDING PROTEIN / galectin / carbohydrate-recognition / LNT / glycosphingolipid / beta sandwich / carbohydrate binding protein | |||||||||
Function / homology | Function and homology information negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / 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 / regulation of T cell apoptotic process / mononuclear cell migration / negative regulation of endocytosis / IgE binding / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / 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 / regulation of T cell apoptotic process / mononuclear cell migration / negative regulation of endocytosis / IgE binding / 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 / regulation of T cell proliferation / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / RNA splicing / neutrophil chemotaxis / 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 / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Collins, P.M. / Blanchard, H. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Galectin-3 interactions with glycosphingolipids. Authors: Collins, P.M. / Bum-Erdene, K. / Yu, X. / Blanchard, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lbm.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lbm.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lbm_validation.pdf.gz | 701.5 KB | Display | wwPDB validaton report |
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Full document | 4lbm_full_validation.pdf.gz | 703.4 KB | Display | |
Data in XML | 4lbm_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 4lbm_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/4lbm ftp://data.pdbj.org/pub/pdb/validation_reports/lb/4lbm | HTTPS FTP |
-Related structure data
Related structure data | 4lbjC 4lbkC 4lblC 4lbnC 4lboC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15758.100 Da / Num. of mol.: 1 / Fragment: unp residues 112-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17931 | ||
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-CL / #4: 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: 2.15 Å3/Da / Density % sol: 42.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 31% PEG 6000, 100MM MGCL2, 8MM BETA MERCEPTOETHANOL, 100MM TRIS HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54184 |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jun 23, 2008 |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.496→42.912 Å / Num. obs: 19413 / % possible obs: 95 % / Redundancy: 5.7 % / Rsym value: 0.046 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.128 / % possible all: 71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1A3K Resolution: 1.55→42.91 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.397 / SU ML: 0.043 / SU R Cruickshank DPI: 0.076 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.074 / 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: 19.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→42.91 Å
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