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- PDB-7b7c: Room temperature X-ray structure of perdeuterated PLL lectin in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7b7c | ||||||
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Title | Room temperature X-ray structure of perdeuterated PLL lectin in complex with L-fucose | ||||||
![]() | PLL lectin | ||||||
![]() | SUGAR BINDING PROTEIN / ![]() ![]() | ||||||
Function / homology | Protein of unknown function DUF346 / Repeat of unknown function (DUF346) / alpha-L-fucopyranose / beta-L-fucopyranose / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M. | ||||||
![]() | ![]() Title: Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions. Authors: Gajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.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 | ![]() | 122.8 KB | Display | ![]() |
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PDB format | ![]() | 76.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7b7eC ![]() 7b7fC ![]() 7bb4C ![]() 7bbcC ![]() 7bbiC ![]() 5c9oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 41944.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Sugar | ChemComp-FUL / ![]() #3: Sugar | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.92 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris/DCl, pD 8.1, 7% (w/v) PEG 8000 dissolved in D2O |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.55→46 Å / Num. obs: 74700 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 18.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.55→1.59 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 5479 / CC1/2: 0.86 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5c9o Resolution: 1.55→39.8 Å / SU ML: 0.1851 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.1986 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→39.8 Å
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Refine LS restraints |
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LS refinement shell |
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