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- PDB-8hyf: Crystal Structure of Banana Lectin In-complex with Fucose at 2.95... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hyf | ||||||
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Title | Crystal Structure of Banana Lectin In-complex with Fucose at 2.95 A Resolution | ||||||
![]() | Ripening-associated protein | ||||||
![]() | SUGAR BINDING PROTEIN / ANTITUMOR PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rasheed, S. / Arif, R. / Huda, N. / Ahmad, M.S. / Mateen, S.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal Structure of Banana Lectin in-Complex with L-Fucose at 2.95 A Resolution Authors: Rasheed, S. / Arif, R. / Huda, N. / Ahmad, M.S. / Mateen, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.9 KB | Display | ![]() |
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PDB format | ![]() | 50.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bmyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/FUC.gif)
![](data/chem/img/FUC.gif)
#1: Protein | Mass: 14577.413 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Sugar | |
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-Non-polymers , 4 types, 125 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-CD / | #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: 4.85 Å3/Da / Density % sol: 74.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25 Details: 1.275 M AMMONIUM SULFATE, 30 mM CADMIUM CHLORIDE, 100 mM TRIS-HCl, PH=8.25 PH range: 8-8.25 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5406 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Nov 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→16.96 Å / Num. obs: 12279 / % possible obs: 99.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.203 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.95→2.95 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1932 / CC1/2: 0.72 / Rrim(I) all: 0.596 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BMY Resolution: 2.95→16.96 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / SU B: 14.223 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.506 / ESU R Free: 0.32 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.722 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→16.96 Å
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Refine LS restraints |
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