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- PDB-6li7: Crystal Structure of Lectin from Pleurotus ostreatus in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6li7 | ||||||
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Title | Crystal Structure of Lectin from Pleurotus ostreatus in complex with GalNAc | ||||||
![]() | Lectin | ||||||
![]() | SUGAR BINDING PROTEIN / Mushroom Lectin / Pleurotus ostreatus Lectin / Carbohydrate Binding Module / C-type letin / Calcium binding protein | ||||||
Function / homology | metal ion binding / 2-acetamido-2-deoxy-beta-D-galactopyranose / Lectin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vajravijayan, S. / Pletnev, S. / Luo, Z. / Ankur, T. / Gunasekaran, K. / Nandhagopal, N. | ||||||
![]() | ![]() Title: Crystallographic and calorimetric analysis on Pleurotus ostreatus lectin and its sugar complexes - promiscuous binding driven by geometry. Authors: Vajravijayan, S. / Pletnev, S. / Luo, Z. / Pletnev, V.Z. / Nandhagopal, N. / Gunasekaran, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.5 KB | Display | ![]() |
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PDB format | ![]() | 64.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kbjC ![]() 6kbqC ![]() 6kc2C ![]() 6likC ![]() 3w5nS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39004.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NGA.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NGA / | |
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-Non-polymers , 3 types, 226 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.26 Å3/Da / Density % sol: 80.36 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.9M Na2HPO4/K2HPO4, pH 5.5, 33% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 2, 2018 Details: Si 111. Rosenbaum-Rock double-crystal monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.098→30 Å / Num. obs: 58637 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.996 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Num. unique obs: 5767 / CC1/2: 0.996 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3W5N Resolution: 2.098→29.642 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.054 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.098 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.103 Å2
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Refinement step | Cycle: LAST / Resolution: 2.098→29.642 Å
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Refine LS restraints |
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LS refinement shell |
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