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- PDB-5y8t: 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: 5y8t | ||||||
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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 | ![]() | 223.5 KB | Display | ![]() |
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PDB format | ![]() | 178.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.1 KB | Display | ![]() |
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Full document | ![]() | 459.1 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x11C ![]() 5x12SC ![]() 5x13C ![]() 5x14C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 5
NCS ensembles :
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Components
#1: Protein | Mass: 21750.912 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 23059 / NRRL B-14472 / W23 / Gene: padR, BSUW23_04210 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 3350, 0.1 M phosphate-citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 56648 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.496 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X12 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.937 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.129 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.861 Å2
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Refinement step | Cycle: 1 / Resolution: 2→30 Å
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Refine LS restraints |
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