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- PDB-7p8u: Crystal Structure of leukotoxin LukE from Staphylococcus aureus i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p8u | ||||||
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Title | Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with p-cresyl sulfate | ||||||
![]() | Leucotoxin LukEv | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lambey, P. / Hoh, F. / Peysson, F. / Granier, S. / Leyrat, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into recognition of chemokine receptors by Staphylococcus aureus leukotoxins. Authors: Lambey, P. / Otun, O. / Cong, X. / Hoh, F. / Brunel, L. / Verdie, P. / Grison, C.M. / Peysson, F. / Jeannot, S. / Durroux, T. / Bechara, C. / Granier, S. / Leyrat, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.3 KB | Display | ![]() |
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PDB format | ![]() | 106.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7p8sC ![]() 7p8tSC ![]() 7p8xC ![]() 7p93C S: Starting model for refinement 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34686.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 266 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/6EI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/6EI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / ![]() | ||
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#3: Chemical | ChemComp-IMD / ![]() | ||
#4: Chemical | ChemComp-SO4 / ![]() | ||
#5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.23 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion Details: 0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→47.65 Å / Num. obs: 48967 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.996 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 2360 / CC1/2: 0.624 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7P8T Resolution: 1.6→47.65 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.08 / SU Rfree Blow DPI: 0.079 / SU Rfree Cruickshank DPI: 0.077
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Displacement parameters | Biso mean: 34.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→47.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.61 Å
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Refinement TLS params. | Origin x: 14.7474 Å / Origin y: -14.4656 Å / Origin z: -12.3236 Å
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Refinement TLS group |
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