+Open data
-Basic information
Entry | Database: PDB / ID: 6yz3 | ||||||
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Title | PqsR (MvfR) in complex with antagonist 19 | ||||||
Components | LysR family transcriptional regulator | ||||||
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 Å | ||||||
Authors | Richardson, W.K. / Emsley, J. | ||||||
Funding support | United Kingdom, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yz3.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yz3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yz3_validation.pdf.gz | 689.3 KB | Display | wwPDB validaton report |
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Full document | 6yz3_full_validation.pdf.gz | 690.4 KB | Display | |
Data in XML | 6yz3_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6yz3_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/6yz3 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/6yz3 | HTTPS FTP |
-Related structure data
Related structure data | 6z07C 6z17C 6z5kC 4jvcS 6q7wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26749.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mvfR, DY930_15985, E4V10_05145, F3H14_28375 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C6ZJJ6 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-Q25 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.508939 Å3/Da / Density % sol: 72.7378 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 100 mM Sodium citrate, 0.2 M Ammonium Acetate and 3% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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→59.73 Å / Num. obs: 10169 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 0.999 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 3→3.18 Å / Rmerge(I) obs: 1.677 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1599 / CC1/2: 0.932 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JVC, 6Q7W Resolution: 3→59.73 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.604 / SU ML: 0.279 / Cross valid method: FREE R-VALUE / ESU R: 0.423 / ESU R Free: 0.319 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 127.924 Å2
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Refinement step | Cycle: LAST / Resolution: 3→59.73 Å
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Refine LS restraints |
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LS refinement shell |
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