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Yorodumi- PDB-7nbw: Crystal structure of PqsR (MvfR) ligand-binding domain in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nbw | ||||||
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Title | Crystal structure of PqsR (MvfR) ligand-binding domain in complex with a pyridin agonist | ||||||
Components | Transcriptional regulator MvfR | ||||||
Keywords | DNA BINDING PROTEIN / QUORUM SENSING / LYSR-TYPE TRANSCRIPTIONAL REGULATOR / PSEUDOMONAS / 2 QUINOLONE SIGNALING SYSTEM / LTTR | ||||||
Function / homology | Function and homology information regulation of transmembrane transport / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å | ||||||
Authors | Schmelz, S. / Blankenfeldt, W. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2021 Title: Divergent synthesis and biological evaluation of 2-(trifluoromethyl)pyridines as virulence-attenuating inverse agonists targeting PqsR. Authors: Schutz, C. / Hodzic, A. / Hamed, M. / Abdelsamie, A.S. / Kany, A.M. / Bauer, M. / Rohrig, T. / Schmelz, S. / Scrima, A. / Blankenfeldt, W. / Empting, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nbw.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nbw.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 7nbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nbw_validation.pdf.gz | 727.7 KB | Display | wwPDB validaton report |
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Full document | 7nbw_full_validation.pdf.gz | 732.5 KB | Display | |
Data in XML | 7nbw_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 7nbw_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/7nbw ftp://data.pdbj.org/pub/pdb/validation_reports/nb/7nbw | HTTPS FTP |
-Related structure data
Related structure data | 2q7vS 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: 25700.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 / Gene: mvfR, PA1003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X0 |
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#2: Chemical | ChemComp-U7Q / ~{ |
#3: 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: 4.75 Å3/Da / Density % sol: 74.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 198mM MgCl2 34.7% MPD 0.1M Tris pH 7.25 10mg/ml PqsR + 1.5 mM 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE 0.39 mM Amaranth (CAS 915-67-3) Cryo: + 20% 2,3- RR- Butandiol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.4769 Å |
Detector | Type: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Oct 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.4769 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→105.124 Å / Num. obs: 15066 / % possible obs: 95.9 % / Redundancy: 56.4 % / Biso Wilson estimate: 72.55 Å2 / CC1/2: 1 / Rpim(I) all: 0.016 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 2.28→2.5 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 753 / CC1/2: 0.73 / Rpim(I) all: 0.667 / % possible all: 86.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2q7v Resolution: 2.28→25.62 Å / SU ML: 0.2831 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.0471 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→25.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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