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Yorodumi- PDB-1kzn: Crystal Structure of E. coli 24kDa Domain in Complex with Clorobiocin -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kzn | ||||||
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Title | Crystal Structure of E. coli 24kDa Domain in Complex with Clorobiocin | ||||||
Components | DNA GYRASE SUBUNIT B | ||||||
Keywords | ISOMERASE / topoisomerase / gyrase B / clorobiocin | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lafitte, D. / Lamour, V. / Tsvetkov, P.O. / Makarov, A.A. / Klich, M. / Deprez, P. / Moras, D. / Briand, C. / Gilli, R. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose. Authors: Lafitte, D. / Lamour, V. / Tsvetkov, P.O. / Makarov, A.A. / Klich, M. / Deprez, P. / Moras, D. / Briand, C. / Gilli, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kzn.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kzn.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kzn ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kzn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22591.369 Da / Num. of mol.: 1 / Fragment: 24 kDa N-terminus domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P06982, UniProt: P0AES6*PLUS, EC: 5.99.1.3 |
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#2: Chemical | ChemComp-CBN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.63 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 20000,propanol-2,HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.938 Å |
Detector | Detector: IMAGE PLATE / Date: Oct 9, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.938 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 16938 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.8 Å2 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 90 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Redundancy: 2.86 % / Rmerge(I) obs: 0.0425 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→14.79 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1321043.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 110.201 Å2 / ksol: 0.479534 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→14.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.239 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.28 / Rfactor Rwork: 0.285 |