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- PDB-6vto: Crystal structure of human Galectin-7 in complex with 4-O-beta-D-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vto | |||||||||||||||||||||
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Title | Crystal structure of human Galectin-7 in complex with 4-O-beta-D-Galactopyranosyl-D-glucose | |||||||||||||||||||||
![]() | Galectin-7 | |||||||||||||||||||||
![]() | SUGAR BINDING PROTEIN / Human Galectin-7 / lactose-furanose | |||||||||||||||||||||
Function / homology | ![]() heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Pham, N.T.H. / Calmettes, C. / Doucet, N. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7. Authors: Pham, N.T.H. / Letourneau, M. / Fortier, M. / Begin, G. / Al-Abdul-Wahid, M.S. / Pucci, F. / Folch, B. / Rooman, M. / Chatenet, D. / St-Pierre, Y. / Lague, P. / Calmettes, C. / Doucet, N. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.8 KB | Display | ![]() |
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PDB format | ![]() | 94.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385.5 KB | Display | ![]() |
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Full document | ![]() | 387.5 KB | Display | |
Data in XML | ![]() | 1.9 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vtpC ![]() 6vtqC ![]() 6vtrC ![]() 6vtsC ![]() 4galS S: Starting model for refinement C: citing same article ( |
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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: 14965.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Sodium Chloride, 0.1 M Tris pH 8, 20 % PEG3350, 5 % Glycerol Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 18, 2019 / Details: 16 tiled fiber-optic tapers |
Radiation | Monochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→45.19 Å / Num. obs: 30152 / % possible obs: 99.11 % / Redundancy: 6.85 % / Biso Wilson estimate: 30.173 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.093 / Net I/σ(I): 15.7 / Num. measured all: 206559 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 7.17 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 3 / Num. measured obs: 21014 / Num. unique obs: 2930 / CC1/2: 0.839 / Rrim(I) all: 0.901 / % possible all: 99.25 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4gal Resolution: 1.69→45.19 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.98 Å2 / Biso mean: 21.037 Å2 / Biso min: 5.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.69→45.19 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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