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- PDB-6zuk: Crystal structure of dimethylated RSL-N23H/G68H (RSL-B6) in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zuk | ||||||||||||
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Title | Crystal structure of dimethylated RSL-N23H/G68H (RSL-B6) in complex with cucurbit[7]uril and zinc | ||||||||||||
![]() | Fucose-binding lectin protein | ||||||||||||
![]() | SUGAR BINDING PROTEIN / cucurbituril / molecular glue / crystal engineering / dimethyllysine / zinc / b-propeller | ||||||||||||
Function / homology | Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / cucurbit[7]uril / Fucose-binding lectin protein![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Guagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / Crowley, P.B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Metal-Mediated Protein-Cucurbituril Crystalline Architectures Authors: Guagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / 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 | ![]() | 141.9 KB | Display | ![]() |
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PDB format | ![]() | 115.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.2 MB | Display | ![]() |
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Full document | ![]() | 6.1 MB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 37.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zulC ![]() 6zumC ![]() 6f7wS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 9719.712 Da / Num. of mol.: 6 / Mutation: N23H, H60S, T67N, G68H, T69G, T70K 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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-Non-polymers , 5 types, 325 molecules ![](data/chem/img/QQ7.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-QQ7 / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-NA / | #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: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3% PEG 8000, 0.1 M BIS-TRIS-HCl pH 7.0, 0.1 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 25, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98013 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.028→43.72 Å / Num. obs: 38198 / % possible obs: 97.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.067 / Rrim(I) all: 0.126 / Net I/σ(I): 7.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6F7W polyalanine Resolution: 2.03→43.72 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.185
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Displacement parameters | Biso max: 104.71 Å2 / Biso mean: 37.19 Å2 / Biso min: 8.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.03→43.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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