+Open data
-Basic information
Entry | Database: PDB / ID: 4jvc | ||||||
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Title | Crystal structure of PqsR co-inducer binding domain | ||||||
Components | Transcriptional regulator MvfR | ||||||
Keywords | TRANSCRIPTION REGULATOR / transcription regulation / co-inducer binding / DNA binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å | ||||||
Authors | Ilangovan, A. / Emsley, J. / Williams, P. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013 Title: Structural basis for native agonist and synthetic inhibitor recognition by the Pseudomonas aeruginosa quorum sensing regulator PqsR (MvfR). Authors: Ilangovan, A. / Fletcher, M. / Rampioni, G. / Pustelny, C. / Rumbaugh, K. / Heeb, S. / Camara, M. / Truman, A. / Chhabra, S.R. / Emsley, J. / Williams, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jvc.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jvc.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jvc_validation.pdf.gz | 442 KB | Display | wwPDB validaton report |
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Full document | 4jvc_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 4jvc_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 4jvc_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/4jvc ftp://data.pdbj.org/pub/pdb/validation_reports/jv/4jvc | HTTPS FTP |
-Related 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: 24288.475 Da / Num. of mol.: 1 / Fragment: co-inducer binding domain, UNP RESIDUES 94-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: mvfR, PA14_51340, PqsR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q02IG8, UniProt: A0A0H2Z7A6*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.93 Å3/Da / Density % sol: 75.06 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Ammonium acetate, 0.1M Tri sodium citrate pH 6.5, 3% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.977 Å | |||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. all: 19299 / Num. obs: 17339 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Biso Wilson estimate: 71.9 Å2 / Rmerge(I) obs: 0.74 / Rsym value: 0.85 / Net I/σ(I): 2 | |||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.5→28.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.112 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.889 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→28.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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