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- PDB-5fry: crystal structure of the phenol-responsive sensory domain of the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fry | |||||||||
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Title | crystal structure of the phenol-responsive sensory domain of the transcription activator PoxR with 3,5-dimethylphenol | |||||||||
![]() | Positive phenol-degradative gene regulator | |||||||||
![]() | TRANSCRIPTION / PHENOL / DMPR / ENHANCER-BINDING PROTEIN / ACTIVATOR / ATPASE FAMILY | |||||||||
Function / homology | ![]() sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Patil, V.V. / Woo, E.J. | |||||||||
![]() | ![]() Title: Structural Analysis of the Phenol-Responsive Sensory Domain of the Transcription Activator Poxr Authors: Patil, V.V. / Park, K.-H. / Lee, S.-G. / Woo, E.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.7 KB | Display | ![]() |
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PDB format | ![]() | 67.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.5 KB | Display | ![]() |
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Full document | ![]() | 476.4 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fruC ![]() 5frvC ![]() 5frwC ![]() 5frxC ![]() 5frzC ![]() 5fs0C 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
#1: Protein | Mass: 23495.096 Da / Num. of mol.: 2 / Fragment: PHENOL BINDING DOMAIN, UNP RESIDUES 1-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.94 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.191 Å / Num. obs: 33213 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 55.11 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.33 / % possible all: 99 |
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Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.792→28.191 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 38.67 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.792→28.191 Å
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Refine LS restraints |
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LS refinement shell |
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