+Open data
-Basic information
Entry | Database: PDB / ID: 1jt0 | ||||||
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Title | Crystal structure of a cooperative QacR-DNA complex | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / multidrug binding protein / cooperative DNA binding / dimer of dimers / TRANSCRIPTION-DNA COMPLEX | ||||||
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 / MIR / Resolution: 2.9 Å | ||||||
Authors | Schumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR. 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jt0.cif.gz | 195.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jt0.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jt0_validation.pdf.gz | 488 KB | Display | wwPDB validaton report |
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Full document | 1jt0_full_validation.pdf.gz | 538.3 KB | Display | |
Data in XML | 1jt0_validation.xml.gz | 35 KB | Display | |
Data in CIF | 1jt0_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jt0 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jt0 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the entire QacR dimer of dimer - DNA complex is contained within the crystallographic asymmetric unit |
-Components
#1: DNA chain | Mass: 8604.564 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 22983.023 Da / Num. of mol.: 4 / Mutation: C72A, C141S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pSK5210 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P0A0N4 #3: Chemical | ChemComp-SO4 / #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: 6.13 Å3/Da / Density % sol: 79.94 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Lithium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Components of the solutions | Name: Li2(SO4) | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→75.73 Å / Num. all: 59396 / Num. obs: 59396 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 144.8 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.06 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.9→3.03 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4414 / Rsym value: 0.52 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 302270 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.9→75.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 12802447.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 86.0326 Å2 / ksol: 0.373149 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→75.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 75.7 Å / σ(F): 0 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 81.5 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.393 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.363 |