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- PDB-5x13: Crystal structure of Bacillus subtilis PadR in complex with p-cou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x13 | ||||||
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Title | Crystal structure of Bacillus subtilis PadR in complex with p-coumaric acid | ||||||
![]() | Transcriptional regulator | ||||||
![]() | TRANSCRIPTION / Transcription factor | ||||||
Function / homology | ![]() Transcription regulator PadR, C-terminal / Virulence activator alpha C-term / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, S.C. / Kwak, Y.M. / Song, W.S. / Hong, M. / Yoon, S.I. | ||||||
![]() | ![]() Title: Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR Authors: Park, S.C. / Kwak, Y.M. / Song, W.S. / Hong, M. / Yoon, S.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.4 KB | Display | ![]() |
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PDB format | ![]() | 69.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.9 KB | Display | ![]() |
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Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x11C ![]() 5x12SC ![]() 5x14C ![]() 5y8tC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21750.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: W23 / Gene: padR, BSUW23_04210 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HC4 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 10 mM p-coumaric acid, 22% PEG 3350, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 23666 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 40.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.224 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X12 Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.506 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.003 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→30 Å
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Refine LS restraints |
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