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- PDB-1jty: Crystal structure of the multidrug binding transcriptional regula... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jty | ||||||
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Title | Crystal structure of the multidrug binding transcriptional regulator QacR bound to ethidium | ||||||
![]() | HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION | ||||||
![]() | TRANSCRIPTION / multidrug binding / multidrug recognition mechanism / cationic lipophilic drugs / QacR / QacA / repressor | ||||||
Function / homology | ![]() DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G. | ||||||
![]() | ![]() Title: Structural mechanisms of QacR induction and multidrug recognition. Authors: Schumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.8 KB | Display | ![]() |
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PDB format | ![]() | 133.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jt6C ![]() 1jtxC ![]() 1jumC ![]() 1jupC ![]() 1jusSC 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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2 | ![]()
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Unit cell |
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Details | QacR is a dimer that binds one drug per dimer. In the crystal there is a drug-free dimer and drug-bound dimer. |
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Components
#1: Protein | Mass: 22983.023 Da / Num. of mol.: 4 / Mutation: C72A, C141S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ET / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2000 / Details: mirrors |
Radiation | Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→83.16 Å / Num. all: 22060 / Num. obs: 22060 / % possible obs: 75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.97→3.15 Å / Redundancy: 4 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3 / Rsym value: 0.229 / % possible all: 67.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JUS Resolution: 2.97→83.16 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 15486414.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 73.0212 Å2 / ksol: 0.37487 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.97→83.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.96→3.15 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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