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- PDB-8q6c: The RSL-D32N - sulfonato-calix[8]arene complex, P63 form, acetate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q6c | ||||||
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Title | The RSL-D32N - sulfonato-calix[8]arene complex, P63 form, acetate pH 4.0 | ||||||
![]() | Fucose-binding lectin protein | ||||||
![]() | SUGAR BINDING PROTEIN / biomaterials / beta-propeller / crystal engineering / molecular glue | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Flood, R.J. / Crowley, P.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Supramolecular Synthons in Protein-Ligand Frameworks. Authors: Flood, R.J. / Mockler, N.M. / Thureau, A. / Malinska, M. / Crowley, P.B. #1: ![]() 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 | ![]() | 43.1 KB | Display | ![]() |
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PDB format | ![]() | 23 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 916.2 KB | Display | ![]() |
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Full document | ![]() | 916.1 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8q6aC ![]() 8q6bC C: citing same article ( |
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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
#1: Protein | Mass: 9732.577 Da / Num. of mol.: 1 / Mutation: D32N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: E7Z57_08365, HF909_06975, HXP36_18875, RSP795_21825, RSP822_19650, RUN39_v1_50103 Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Sugar | ChemComp-BDF / |
#4: Chemical | ChemComp-EVB / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.83 % |
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Crystal grow | Temperature: 277.15 K / Method: batch mode / pH: 4 / Details: 20 mM sodium acetate pH 4.0, 50 mM NaCl |
-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: Nov 16, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→59.82 Å / Num. obs: 26994 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 17.7 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.079 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.38→1.41 Å / Redundancy: 15.3 % / Num. unique obs: 1327 / CC1/2: 0.884 / Rpim(I) all: 0.323 / Rrim(I) all: 1.269 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→51.81 Å
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Refine LS restraints |
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LS refinement shell |
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