+Open data
-Basic information
Entry | Database: PDB / ID: 6z5k | ||||||
---|---|---|---|---|---|---|---|
Title | PqsR (MvfR) in complex with antagonist 18 | ||||||
Components | Transcriptional regulator MvfR | ||||||
Keywords | DNA BINDING PROTEIN / Pseudomonas aeruginosa / Antagonist / Quorum sensing | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å | ||||||
Authors | Richardson, W.K. / Emsley, J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Novel quinazolinone inhibitors of the Pseudomonas aeruginosa quorum sensing transcriptional regulator PqsR. Authors: Grossman, S. / Soukarieh, F. / Richardson, W. / Liu, R. / Mashabi, A. / Emsley, J. / Williams, P. / Camara, M. / Stocks, M.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6z5k.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6z5k.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z5k_validation.pdf.gz | 685.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6z5k_full_validation.pdf.gz | 686 KB | Display | |
Data in XML | 6z5k_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 6z5k_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/6z5k ftp://data.pdbj.org/pub/pdb/validation_reports/z5/6z5k | HTTPS FTP |
-Related structure data
Related structure data | 6yz3C 6z07C 6z17C 4jvcS 6q7wS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26749.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: mvfR, PA14_51340 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2Z7A6 |
---|---|
#2: Chemical | ChemComp-QAE / |
#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: 4.38 Å3/Da / Density % sol: 71.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM Sodium citrate, 200 mM Ammonium acetate and 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→115.46 Å / Num. obs: 7628 / % possible obs: 92.4 % / Redundancy: 9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 3.2→3.42 Å / Rmerge(I) obs: 0.398 / Num. unique obs: 1370 / CC1/2: 0.972 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JVC, 6Q7W Resolution: 3.201→76.972 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 21.83 / SU ML: 0.345 / Cross valid method: FREE R-VALUE / ESU R: 1.045 / ESU R Free: 0.418 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 134.248 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.201→76.972 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|