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- PDB-7alf: The dimethylated RSL - sulfonato-calix[8]arene complex, P3 form, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7alf | ||||||
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Title | The dimethylated RSL - sulfonato-calix[8]arene complex, P3 form, acetate pH 4.0 | ||||||
![]() | Fucose-binding lectin protein | ||||||
![]() | SUGAR BINDING PROTEIN / calixarene / protein framework / cage / crystal engineering / molecular glue / synthetic receptor / macrocycle / biomaterial | ||||||
Function / homology | Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / beta-D-fructopyranose / sulfonato-calix[8]arene / Fucose-binding lectin protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramberg, K. / Engilberge, S. / Crowley, P.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Facile Fabrication of Protein-Macrocycle Frameworks. Authors: Ramberg, K.O. / Engilberge, S. / Skorek, T. / Crowley, P.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.2 KB | Display | ![]() |
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PDB format | ![]() | 66 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6z5gC ![]() 6z5mC ![]() 6z5pC ![]() 6z5qC ![]() 6z5wC ![]() 6z5xC ![]() 6z5zC ![]() 6z60C ![]() 6z62C ![]() 7algC ![]() 2bt9S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 9842.753 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Sugar | ChemComp-BDF / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 277.15 K / Method: batch mode / pH: 4 Details: 20 mM sodium acetate 50 mM NaCl 5 mM D-fructose 10 mM sclx8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→64.72 Å / Num. obs: 68362 / % possible obs: 99 % / Redundancy: 1 % / CC1/2: 1 / Rpim(I) all: 0.28 / Rrim(I) all: 0.61 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 2.9 % / Num. unique obs: 3377 / CC1/2: 0.92 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BT9 Resolution: 1.261→40.303 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2.11 / Phase error: 16.42 / Stereochemistry target values: ML
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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 max: 109.77 Å2 / Biso mean: 19.6227 Å2 / Biso min: 10.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.261→40.303 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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