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Yorodumi- PDB-3qp8: Crystal structure of CviR (Chromobacterium violaceum 12472) ligan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qp8 | ||||||
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Title | Crystal structure of CviR (Chromobacterium violaceum 12472) ligand-binding domain bound to C10-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 / quorum sensing transcription receptor / N-decanoyl-L-Homoserine lactone | ||||||
Function / homology | Function and homology information quorum sensing / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 3qp8.cif.gz | 300.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qp8.ent.gz | 246.3 KB | Display | PDB format |
PDBx/mmJSON format | 3qp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qp8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3qp8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3qp8_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 3qp8_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/3qp8 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/3qp8 | HTTPS FTP |
-Related structure data
Related structure data | 3qp1C 3qp2C 3qp4C 3qp5C 3qp6SC 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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Unit cell |
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-Components
#1: Protein | Mass: 20314.945 Da / Num. of mol.: 4 / Fragment: ligand binding domain (UNP residues 8-187) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: 12472 / Gene: cviR / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Plyss / References: UniProt: Q7NQP7 #2: Chemical | ChemComp-HL0 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 100 mM CHES, 1 M sodium citrate, pH 9.5, 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: 1.0809 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→70.71 Å / Num. obs: 101162 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.043 / Net I/σ(I): 16.678 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.25 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QP6 Resolution: 1.6→70.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.879 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.095 / 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 max: 77.59 Å2 / Biso mean: 36.043 Å2 / Biso min: 12.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→70.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.596→1.638 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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