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- PDB-3qdu: Structure of Boletus edulis lectin in complex with N,N-diacetyl c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qdu | |||||||||
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Title | Structure of Boletus edulis lectin in complex with N,N-diacetyl chitobiose | |||||||||
![]() | BOLETUS EDULIS LECTIN | |||||||||
![]() | SUGAR BINDING PROTEIN / Boletus edulis / lectin / mushroom / T-antigen disaccharide / N / N-diacetyl chitobiose / Carbohydrate / Sugar Binding | |||||||||
Function / homology | Fungal fruit body lectin / Fungal fruit body lectin / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / carbohydrate binding / Sandwich / Mainly Beta / Boletus edulis lectin![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bovi, M. / Carrizo, M.E. / Capaldi, S. / Perduca, M. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L. | |||||||||
![]() | ![]() Title: Structure of a lectin with antitumoral properties in king bolete (Boletus edulis) mushrooms. Authors: Bovi, M. / Carrizo, M.E. / Capaldi, S. / Perduca, M. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243 KB | Display | ![]() |
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PDB format | ![]() | 197.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qdsC ![]() 3qdtC ![]() 3qdvC ![]() 3qdwSC ![]() 3qdxC ![]() 3qdyC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15851.834 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M magnesium acetate, 0.1M sodium cacodylate, 10% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2007 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.7 Å / Num. obs: 47335 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 6.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QDW Resolution: 2→39.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.213 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2→39.67 Å
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Refine LS restraints |
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