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Yorodumi- PDB-3br3: Crystal Structure of the Complex of Ethidium Bound to QacR(E90Q),... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3br3 | ||||||
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Title | Crystal Structure of the Complex of Ethidium Bound to QacR(E90Q), a Mutant of a Multidrug Binding Transcriptional Repressor | ||||||
Components | HTH-type transcriptional regulator qacR | ||||||
Keywords | TRANSCRIPTION / QacR / multidrug resistance / TetR / ethidium / DNA-binding / Repressor / Transcription regulation | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Brooks, B.E. | ||||||
Citation | Journal: To be Published Title: Formal electrostatic interactions do not govern QacR-cation affinity Authors: Brooks, B.E. / Hardie, K.M. / Brown, M.H. / Skurray, R.A. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3br3.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3br3.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 3br3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/3br3 ftp://data.pdbj.org/pub/pdb/validation_reports/br/3br3 | HTTPS FTP |
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-Related structure data
Related structure data | 3bqzC 3br0C 3br1C 3br2C 3br5C 3br6C 1jt6S 3br4 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22939.936 Da / Num. of mol.: 2 / Mutation: K67S,C72A,E90Q,C141S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: qacR / Plasmid: pTTQ18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P0A0N3 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ET / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.43 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1:1 10mg/ml protein with 2.3M Ammonium sulfate with 100mM Sodium Acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jun 15, 2007 Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.04 Å / Num. all: 15047 / Num. obs: 15047 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.9 / Redundancy: 7.52 % / Rsym value: 0.061 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.45 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1517 / Rsym value: 0.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JT6 Resolution: 2.8→41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.898 / SU B: 30.927 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.1 / ESU R Free: 0.412 / Stereochemistry target values: Engh & Huber / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.77 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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