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Open data
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Basic information
Entry | Database: PDB / ID: 5bs8 | ||||||
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Title | Crystal structure of a topoisomerase II complex | ||||||
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![]() | Isomerase/DNA / protein-DNA complex / topoisomerase II / Isomerase-DNA complex | ||||||
Function / homology | ![]() DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blower, T.R. / Williamson, B.H. / Kerns, R.J. / Berger, J.M. | ||||||
![]() | ![]() Title: Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis. Authors: Blower, T.R. / Williamson, B.H. / Kerns, R.J. / Berger, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 955.7 KB | Display | ![]() |
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PDB format | ![]() | 804 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 56.5 KB | Display | |
Data in CIF | ![]() | 78.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5btaC ![]() 5btcC ![]() 5btdC ![]() 5btfC ![]() 5btgC ![]() 5btiC ![]() 5btlC ![]() 5btnC ![]() 2xkkS 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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Unit cell |
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Details | The double-stranded DNAs are superposed copies of each other, overlaid in opposite orientations (because directionality could not be resolved). Therefore in reality, rather than in the model, the biological assembly would in fact be hexameric - four proteins and one double-stranded DNA. |
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Components
-DNA gyrase subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 56209.422 Da / Num. of mol.: 2 / Fragment: GyrA tower and C-gate domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: gyrA, Rv0006, MTCY10H4.04 / Plasmid: pET-28b / Production host: ![]() ![]() #2: Protein | Mass: 28272.412 Da / Num. of mol.: 2 / Fragment: GyrB toprim domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: gyrB, Rv0005, MTCY10H4.03 / Plasmid: pET-28b / Production host: ![]() ![]() |
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-DNA substrate 24-mer ... , 2 types, 4 molecules EHFG
#3: DNA chain | Mass: 7417.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: DNA chain | Mass: 7319.739 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 409 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/MFX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MFX.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.58 % / Description: Very thin planar crystals (<10 uM thick), up to 200 x 300 uM2 surface area |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Tris-HCl, 13-15% PEG 4000, 200 mM MgCl2, 6.25% PEG 400 PH range: 7.0 to 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2014 |
Radiation | Monochromator: Si 220 filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.399→102.3 Å / Num. obs: 83492 / % possible obs: 97.68 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08799 / Net I/σ(I): 10.66 |
Reflection shell | Resolution: 2.399→2.485 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.99 / Rejects: 0 / % possible all: 93.22 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XKK Resolution: 2.399→102.252 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 26.98 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 319.72 Å2 / Biso mean: 77.0026 Å2 / Biso min: 27.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.399→102.252 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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