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Yorodumi- PDB-3qp6: Crystal structure of CviR (Chromobacterium violaceum 12472) bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qp6 | ||||||
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Title | Crystal structure of CviR (Chromobacterium violaceum 12472) bound to C6-HSL | ||||||
Components | CviR transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / quorum sensing / agonist / antagonist / LuxR / acylated homoserine lactone / transcription factor / DNA binding protein / ligand binding domain / signal receptor / N-hexanoyl-L-homoserine lactone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chen, G. / Swem, L. / Swem, D. / Stauff, D. / O'Loughlin, C. / Jeffrey, P. / Bassler, B. / Hughson, F. | ||||||
Citation | Journal: Mol.Cell / Year: 2011 Title: A strategy for antagonizing quorum sensing. Authors: Chen, G. / Swem, L.R. / Swem, D.L. / Stauff, D.L. / O'Loughlin, C.T. / Jeffrey, P.D. / Bassler, B.L. / Hughson, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qp6.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qp6.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/3qp6 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/3qp6 | HTTPS FTP |
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-Related structure data
Related structure data | 3qp1C 3qp2C 3qp4C 3qp5C 3qp8C 3qp7 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29560.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: 12472 / Gene: cviR / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plyss / References: UniProt: Q7NQP7 |
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#2: Chemical | ChemComp-HL6 / |
#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: 2.32 Å3/Da / Density % sol: 47.04 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM imidazole, 10% w/v PEG5000 MME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0401 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0401 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 20522 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.071 / Net I/σ(I): 17.127 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.656 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QP7 3qp7 Resolution: 2→26.536 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.116 Å2 / ksol: 0.323 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→26.536 Å
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Refine LS restraints |
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LS refinement shell |
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