+Open data
-Basic information
Entry | Database: PDB / ID: 6l6b | ||||||
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Title | X-ray structure of human galectin-10 in complex with L-fucose | ||||||
Components | Galectin-10CLC (gene) | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-sandwich structure / lectin | ||||||
Function / homology | Function and homology information regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate binding / collagen-containing extracellular matrix / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Authors | Kamitori, S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structures of human galectin-10/monosaccharide complexes demonstrate potential of monosaccharides as effectors in forming Charcot-Leyden crystals. Authors: Itoh, A. / Nonaka, Y. / Nakakita, S.I. / Yoshida, H. / Nishi, N. / Nakamura, T. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l6b.cif.gz | 48.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l6b.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 6l6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/6l6b ftp://data.pdbj.org/pub/pdb/validation_reports/l6/6l6b | HTTPS FTP |
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-Related structure data
Related structure data | 6l64C 6l67C 6l68C 6l6aC 6l6cC 6l6dC 1qkqS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16644.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Production host: Escherichia coli (E. coli) / References: UniProt: Q05315 |
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#2: Sugar | ChemComp-FUL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.55 Å / Num. obs: 18129 / % possible obs: 99.5 % / Redundancy: 18.6 % / CC1/2: 0.997 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.8→1.85 Å / Num. unique obs: 1223 / CC1/2: 0.977 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QKQ Resolution: 1.802→19.546 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.71 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.126 Details: Hydrogens have been added in their 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.868 Å2
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Refinement step | Cycle: LAST / Resolution: 1.802→19.546 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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