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Open data
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Basic information
Entry | Database: PDB / ID: 6.0E+20 | |||||||||
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Title | Crystal structure of the Dario rerio galectin-1-L2 | |||||||||
![]() | Galectin | |||||||||
![]() | SUGAR BINDING PROTEIN / Galectin-1 / innate immunity infectious hematopoietic necrosis virus (IHNV) / Danio rerio / zebrafish | |||||||||
Function / homology | ![]() galactoside binding / vasculature development / sprouting angiogenesis / positive regulation of neurogenesis / positive regulation of wound healing / skeletal muscle fiber development / laminin binding / carbohydrate binding / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ghosh, A. / Bianchet, M.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the zebrafish galectin-1-L2 and model of its interaction with the infectious hematopoietic necrosis virus (IHNV) envelope glycoprotein. Authors: Ghosh, A. / Banerjee, A. / Amzel, L.M. / Vasta, G.R. / Bianchet, M.A. #1: ![]() Title: Soluble beta-galactosyl-binding lectin (galectin) from toad ovary: crystallographic studies of two protein-sugar complexes. Authors: Bianchet, M.A. / Ahmed, H. / Vasta, G.R. / Amzel, L.M. #2: Journal: J. Biol. Chem. / Year: 2013 Title: The galectin CvGal1 from the eastern oyster (Crassostrea virginica) binds to blood group A oligosaccharides on the hemocyte surface. Authors: Feng, C. / Ghosh, A. / Amin, M.N. / Giomarelli, B. / Shridhar, S. / Banerjee, A. / Fernandez-Robledo, J.A. / Bianchet, M.A. / Wang, L.X. / Wilson, I.B. / Vasta, G.R. #3: Journal: Biochemistry / Year: 2015 Title: Galectin CvGal2 from the Eastern Oyster (Crassostrea virginica) Displays Unique Specificity for ABH Blood Group Oligosaccharides and Differentially Recognizes Sympatric Perkinsus Species. Authors: Feng, C. / Ghosh, A. / Amin, M.N. / Bachvaroff, T.R. / Tasumi, S. / Pasek, M. / Banerjee, A. / Shridhar, S. / Wang, L.X. / Bianchet, M.A. / Vasta, G.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ganS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15421.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 0.2 M Magnesium Chloride Hexahydrate, 30% (v/v) PolyethG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. obs: 18718 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 1262 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GAN Resolution: 2→34.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.772 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.174 / 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: 29.813 Å2
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Refinement step | Cycle: 1 / Resolution: 2→34.81 Å
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Refine LS restraints |
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