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- PDB-2xcs: The 2.1A crystal structure of S. aureus Gyrase complex with GSK29... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xcs | ||||||
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Title | The 2.1A crystal structure of S. aureus Gyrase complex with GSK299423 and DNA | ||||||
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![]() | ISOMERASE / TYPE IIA TOPOISOMERASE | ||||||
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 | ![]() ![]() SYNTHETIC CONSTRUCT (others) | ||||||
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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PDBx/mmCIF format | ![]() | 325.1 KB | Display | ![]() |
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PDB format | ![]() | 257.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xcoC ![]() 2xcqSC ![]() 2xcrC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 78109.000 Da / Num. of mol.: 2 Fragment: GYRB- C-TERMINAL 27KDA DOMAIN, RESIDUES 410-543 AND 580-644, GYRA- N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491 Mutation: YES Source method: isolated from a genetically manipulated source Details: C-TERMINUS GYRB (644) FUSED TO N-TERMINUS GYRA (1002). GREEK KEY DOMAIN (544-579) DELETED AND REPLACED WITH TWO RESIDUES, TG Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 6099.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-RXV / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | MANGANESE ION (MN): MN2+ ION | Sequence details | GREEK KEY DOMAIN (544-579) DELETED AND REPLACED WITH TWO RESIDUES, TG CATALYTIC TYROSINE (1123) ...GREEK KEY DOMAIN (544-579) DELETED AND REPLACED WITH TWO RESIDUES, TG CATALYTIC TYROSINE (1123) MUTATED TO PHENYLALAN | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.48 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 18% PEG 5000MME, 0.1 M BISTRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 113168 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 28.25 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.6 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XCQ Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.114 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. COMPOUND SITS ON TWOFOLD AXIS OF THE DIMER. TO SEE BINDING MODE OF SINGLE COMPOUND DELETE B CONFORMERS OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. COMPOUND SITS ON TWOFOLD AXIS OF THE DIMER. TO SEE BINDING MODE OF SINGLE COMPOUND DELETE B CONFORMERS OF COMPOUND AND SIDE-CHAINS B83, B121, D83, D121.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.417 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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