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- PDB-2xcq: The 2.98A crystal structure of the catalytic core (B'A' region) o... -
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Basic information
Entry | Database: PDB / ID: 2xcq | ||||||
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Title | The 2.98A crystal structure of the catalytic core (B'A' region) of Staphylococcus aureus DNA Gyrase | ||||||
![]() | DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A | ||||||
![]() | ISOMERASE | ||||||
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 / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP 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 / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. ...Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / Lewis, C.J. / May, E.W. / Singh, O. / Spitzfaden, C. / Shen, C. / Shillings, A. / Theobald, A.F. / Wohlkonig, A. / Pearson, N.D. / Gwynn, M.N. | ||||||
![]() | ![]() Title: Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents. Authors: Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / ...Authors: Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / Lewis, C.J. / May, E.W. / Saunders, M.R. / Singh, O. / Spitzfaden, C. / Shen, C. / Shillings, A. / Theobald, A.F. / Wohlkonig, A. / Pearson, N.D. / Gwynn, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142 KB | Display | ![]() |
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PDB format | ![]() | 109.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xcoSC ![]() 2xcrC ![]() 2xcsC ![]() 2xctC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 82344.898 Da / Num. of mol.: 1 Fragment: C-TERMINAL 27KDA DOMAIN, RESIDUES 410-644, N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491 Source method: isolated from a genetically manipulated source Details: C-TERMINUS GYRB (A644) FUSED TO N-TERMINUS GYRA (A1002) Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.33 % / Description: NONE |
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Crystal grow | Details: 12.75% PEG 3350, 85MM MGFORMATE, 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93926 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→14 Å / Num. obs: 19434 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 99 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.98→3.14 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XCO Resolution: 2.98→13.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.879 / SU B: 21.572 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.425 Å2
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Refinement step | Cycle: LAST / Resolution: 2.98→13.99 Å
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Refine LS restraints |
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