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Yorodumi- PDB-7p8u: Crystal Structure of leukotoxin LukE from Staphylococcus aureus i... -
+Open data
-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 | ||||||
Components | Leucotoxin LukEv | ||||||
Keywords | TOXIN / leukotoxin / beta barrel pore forming toxin / cytolysis / hemolysis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Lambey, P. / Hoh, F. / Peysson, F. / Granier, S. / Leyrat, C. | ||||||
Funding support | France, 1items
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Citation | Journal: Elife / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p8u.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p8u.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 7p8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p8u_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7p8u_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7p8u_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 7p8u_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/7p8u ftp://data.pdbj.org/pub/pdb/validation_reports/p8/7p8u | HTTPS FTP |
-Related structure data
Related structure data | 7p8sC 7p8tSC 7p8xC 7p93C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Staphylococcus aureus (bacteria) / Gene: lukEv, SAOUHSC_01955 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FXB0 |
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-Non-polymers , 5 types, 266 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96545 Å |
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: 0.96545 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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