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Yorodumi- PDB-6vc3: Peanut lectin complexed with S-beta-D-thiogalactopyranosyl 6-deox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vc3 | |||||||||
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Title | Peanut lectin complexed with S-beta-D-thiogalactopyranosyl 6-deoxy-6-S-propynyl-beta-D-glucopyranoside (STG) | |||||||||
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: 1.95 Å | |||||||||
Authors | Otero, L.H. / Primo, E.D. / Cagnoni, A.J. / Cano, M.E. / 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 | 6vc3.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vc3.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 6vc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vc3_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
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Full document | 6vc3_full_validation.pdf.gz | 423.3 KB | Display | |
Data in XML | 6vc3_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6vc3_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/6vc3 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/6vc3 | HTTPS FTP |
-Related structure data
Related structure data | 6v95C 6vavC 6vawC 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 | #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: 3.04 Å3/Da / Density % sol: 59.47 % |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
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: 1.95→49.03 Å / Num. obs: 82675 / % possible obs: 92.8 % / Redundancy: 9.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.039 / Rrim(I) all: 0.127 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2 / Num. unique obs: 4496 / CC1/2: 0.757 / Rpim(I) all: 0.254 / Rrim(I) all: 0.846 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PEL Resolution: 1.95→49.03 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.172
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Displacement parameters | Biso max: 175.73 Å2 / Biso mean: 37.57 Å2 / Biso min: 10.99 Å2
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Refinement step | Cycle: final / Resolution: 1.95→49.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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