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Yorodumi- PDB-6v95: Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v95 | |||||||||
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Title | Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L-tartaramidoyl derivative (diNGT) | |||||||||
Components | Galactose-binding lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / Beta-galactosylamides / Beta-thiogalactosides / Peanut agglutinin / Glycomimetics | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Arachis hypogaea (peanut) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | |||||||||
Authors | Otero, L.H. / Primo, E.D. / Cagnoni, A.J. / Klinke, S. / Goldbaum, F.A. / Uhrig, M.L. | |||||||||
Funding support | Argentina, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v95.cif.gz | 221.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v95.ent.gz | 175.9 KB | Display | PDB format |
PDBx/mmJSON format | 6v95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/6v95 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/6v95 | HTTPS FTP |
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-Related structure data
Related structure data | 6vavC 6vawC 6vc3C 6vc4C 6vgfC 2pelS S: Starting model for refinement C: citing same article (ref.) |
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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: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: P02872 #2: Chemical | ChemComp-QSG / ( #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.86 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 15% (w/v) PEG 8000, 0.1M sodium citrate, 0.1M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2018 / Details: KIRKPATRICK-BAEZ PAIR OF BIMORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→48.82 Å / Num. obs: 116267 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.029 / Rrim(I) all: 0.079 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5724 / CC1/2: 0.844 / Rpim(I) all: 0.328 / Rrim(I) all: 0.91 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PEL Resolution: 1.78→26.06 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.115
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Displacement parameters | Biso max: 186.55 Å2 / Biso mean: 36.56 Å2 / Biso min: 14.24 Å2
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Refinement step | Cycle: final / Resolution: 1.78→26.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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