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Open data
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Basic information
Entry | Database: PDB / ID: 7p8h | ||||||
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Title | chicken GRIFIN bound to blood group tetrasaccharide B (type 1) | ||||||
![]() | Galectin | ||||||
![]() | SUGAR BINDING PROTEIN / GRIFIN / Galactoside-binding lectin / Blood group B type 1 antigen / beta anomer | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruiz, F.M. / Romero, A. | ||||||
![]() | ![]() Title: Structural Characterization of Rat Galectin-5, an N-Tailed Monomeric Proto-Type-like Galectin. Authors: Ruiz, F.M. / Medrano, F.J. / Ludwig, A.K. / Kaltner, H. / Shilova, N.V. / Bovin, N.V. / Gabius, H.J. / Romero, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.6 KB | Display | ![]() |
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PDB format | ![]() | 156.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jp5C ![]() 5jpgC ![]() 5nmjS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16205.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 691.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Blood group B type 1 antigen, beta anomer / References: BIRD: PRD_002353 #3: Water | ChemComp-HOH / | Compound details | B Type 1, blood group B type 1 tetrasaccharide, alpha-D-Galp-(1->3)-[alpha-L-Fucp-(1->2)]-beta-D- ...B Type 1, blood group B type 1 tetrasaccharide, alpha-D-Galp-(1->3)-[alpha-L-Fucp-(1->2)]-beta-D-Galp-(1->3)-beta-D-GlcpNAc | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 15 % w/v Polyethylene glycol 400; 100 mM MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→43.85 Å / Num. obs: 90857 / % possible obs: 99.13 % / Redundancy: 2 % / Biso Wilson estimate: 9.99 Å2 / CC1/2: 0.9 / Rmerge(I) obs: 0.015 / Rrim(I) all: 0.021 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.13→1.17 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2 / Num. unique obs: 8884 / CC1/2: 0.9 / Rrim(I) all: 0.431 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NMJ Resolution: 1.13→43.85 Å / SU ML: 0.1521 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9823 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 14.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→43.85 Å
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Refine LS restraints |
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LS refinement shell |
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