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- PDB-1jup: Crystal structure of the multidrug binding transcriptional repres... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jup | ||||||
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Title | Crystal structure of the multidrug binding transcriptional repressor QacR bound to malachite green | ||||||
![]() | HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION | ||||||
![]() | TRANSCRIPTION / multidrug recognition / malachite green / QacR / multidrug binding protein | ||||||
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 | ![]() | 164.3 KB | Display | ![]() |
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PDB format | ![]() | 132.6 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 ![]() 1jtyC ![]() 1jumC ![]() 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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2 | ![]()
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Unit cell |
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Details | QacR is a dimer and there are two QacR dimers in the ASU one bound with the determined drug binding stoichiometry of one drug per 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-MGR / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.04 % |
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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: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 23, 2000 / Details: yale mirrors |
Radiation | Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→64.6 Å / Num. all: 26023 / Num. obs: 26023 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.95→3.1 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.278 / % possible all: 78 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JUS Resolution: 2.95→64.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1038053.03 / 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: 43.9022 Å2 / ksol: 0.331763 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→64.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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