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- PDB-6z5m: The RSL - sulfonato-calix[8]arene complex, I23 form, Gly-HCl pH 2.2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6z5m | ||||||
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Title | The RSL - sulfonato-calix[8]arene complex, I23 form, Gly-HCl pH 2.2 | ||||||
![]() | 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 | ![]() | 45.4 KB | Display | ![]() |
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PDB format | ![]() | 30.4 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 ![]() 6z5pC ![]() 6z5qC ![]() 6z5wC ![]() 6z5xC ![]() 6z5zC ![]() 6z60C ![]() 6z62C ![]() 7alfC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 9733.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103 Production host: ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 69.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 2.2 Details: 0.1 M Gly-HCl pH 2.2, 0.8 M Ammonium sulfate, 0.2 M Magnesium chloride, 0.01 M sulfonato-calix[8]arene |
-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: Jan 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: 1.6→73.26 Å / Num. obs: 24491 / % possible obs: 99.8 % / Redundancy: 34.5 % / CC1/2: 1 / Rpim(I) all: 0.15 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1173 / CC1/2: 0.857 / Rpim(I) all: 0.243 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BT9 Resolution: 1.6→51.806 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 16.07 / 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: 77.69 Å2 / Biso mean: 25.174 Å2 / Biso min: 11.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→51.806 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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