[English] 日本語
Yorodumi- PDB-7p93: Crystal Structure of leukotoxin LukE from Staphylococcus aureus i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p93 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a sulfated ACKR1 N-terminal peptide | ||||||
Components |
| ||||||
Keywords | TOXIN / leukotoxin / beta barrel pore forming toxin / cytolysis / hemolysis | ||||||
Function / homology | Function and homology information regulation of chemokine production / cytolysis in another organism / C-C chemokine binding / chemokine-mediated signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor activity / recycling endosome / defense response / transmembrane signaling receptor activity / signaling receptor activity ...regulation of chemokine production / cytolysis in another organism / C-C chemokine binding / chemokine-mediated signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor activity / recycling endosome / defense response / transmembrane signaling receptor activity / signaling receptor activity / toxin activity / early endosome / inflammatory response / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Lambey, P. / Hoh, F. / Peysson, F. / Granier, S. / Leyrat, C. | ||||||
Funding support | France, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7p93.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7p93.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 7p93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/7p93 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/7p93 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7p8sSC 7p8tC 7p8uC 7p8xC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#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 | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 1505.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16570 #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.77 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 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: 0.96546 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→47.16 Å / Num. obs: 51899 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.998 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.55→1.58 Å / Num. unique obs: 2552 / CC1/2: 0.622 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7P8S Resolution: 1.55→47.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.071 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.071
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.13 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→47.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.56 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Origin x: 15.2077 Å / Origin y: -14.5851 Å / Origin z: -13.0666 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|* } |