+Open data
-Basic information
Entry | Database: PDB / ID: 5t7u | ||||||
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Title | Crystal structure of galectin-8N in complex with Glycerol | ||||||
Components | Galectin-8 | ||||||
Keywords | SUGAR BINDING PROTEIN / carbohydrate-binding protein / galectin-8 lectin | ||||||
Function / homology | Function and homology information lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / extracellular space / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Bohari, M.H. / Yu, X. / Blanchard, H. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structure-based rationale for differential recognition of lacto- and neolacto- series glycosphingolipids by the N-terminal domain of human galectin-8. Authors: Bohari, M.H. / Yu, X. / Zick, Y. / Blanchard, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t7u.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t7u.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 5t7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/5t7u ftp://data.pdbj.org/pub/pdb/validation_reports/t7/5t7u | HTTPS FTP |
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-Related structure data
Related structure data | 5t7iC 5t7sC 5t7tC 3ap5S 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: 17586.322 Da / Num. of mol.: 1 / Fragment: N-terminal Domaine (UNP residues 1-155) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: 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: 2.35 Å3/Da / Density % sol: 47.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→40.73 Å / Num. obs: 23530 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AP5 Resolution: 1.58→40.73 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.866 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.643 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→40.73 Å
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Refine LS restraints |
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