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- PDB-6vc4: Peanut lectin complexed with S-beta-D-Thiogalactopyranosyl beta-D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vc4 | |||||||||
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Title | Peanut lectin complexed with S-beta-D-Thiogalactopyranosyl beta-D-glucopyranoside derivative (STGD) | |||||||||
![]() | Galactose-binding lectin | |||||||||
![]() | SUGAR BINDING PROTEIN / Beta-galactosylamides / Beta-thiogalactosides / Peanut agglutinin / Glycomimetics | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Otero, L.H. / Primo, E.D. / Cagnoni, A.J. / Cano, M.E. / Klinke, S. / Goldbaum, F.A. / Uhrig, M.L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of peanut lectin in the presence of synthetic beta-N- and beta-S-galactosides disclose evidence for the recognition of different glycomimetic ligands. Authors: Cagnoni, A.J. / Primo, E.D. / Klinke, S. / Cano, M.E. / Giordano, W. / Marino, K.V. / Kovensky, J. / Goldbaum, F.A. / Uhrig, M.L. / Otero, L.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.6 KB | Display | ![]() |
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PDB format | ![]() | 169.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463 KB | Display | ![]() |
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Full document | ![]() | 465.2 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v95C ![]() 6vavC ![]() 6vawC ![]() 6vc3C ![]() 6vgfC ![]() 2pelS 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: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-QWG / ( #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: 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: 2.99 Å3/Da / Density % sol: 58.83 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 15% (w/v) PEG 8000, 0.1 sodium citrate, 0.125M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2017 Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS |
Radiation | Monochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→62.28 Å / Num. obs: 95802 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.04 / Rrim(I) all: 0.135 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4660 / CC1/2: 0.832 / Rpim(I) all: 0.314 / Rrim(I) all: 1.06 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PEL Resolution: 1.9→56.64 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.133
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Displacement parameters | Biso max: 144.11 Å2 / Biso mean: 35.02 Å2 / Biso min: 12.35 Å2
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Refinement step | Cycle: final / Resolution: 1.9→56.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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