+Open data
-Basic information
Entry | Database: PDB / ID: 6c28 | ||||||
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Title | Transcriptional repressor, CouR, bound to p-coumaroyl-CoA | ||||||
Components | Transcriptional regulator, MarR family | ||||||
Keywords | DNA BINDING PROTEIN / Transcriptional regulation / repressor / MarR family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Cogan, D.P. / Nair, S.K. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural basis of transcriptional regulation by CouR, a repressor of coumarate catabolism, inRhodopseudomonas palustris. Authors: Cogan, D.P. / Baraquet, C. / Harwood, C.S. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c28.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c28.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 6c28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c28_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6c28_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6c28_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 6c28_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/6c28 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/6c28 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20253.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic) Strain: ATCC BAA-98 / CGA009 / Gene: couR, RPA1794 / Plasmid: pET28-MBP / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Rosetta / References: UniProt: Q6N8V9 #2: Chemical | ChemComp-WCA / #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: 2.26 Å3/Da / Density % sol: 45.58 % / Description: thick rods |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.17 M lithium sulfate, 23.5% PEG 4K, 1 mM DTT, 0.085 M Tris-HCl pH 8.5, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→128.801 Å / Num. obs: 43271 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.09→2.126 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2130 / CC1/2: 0.8 / Rpim(I) all: 0.392 / Rrim(I) all: 1.029 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→80.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.086 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.194 / 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: 48.386 Å2
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Refinement step | Cycle: 1 / Resolution: 2.09→80.92 Å
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