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- PDB-5d7c: Crystal structure of the ATP binding domain of S. aureus GyrB com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d7c | ||||||
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Title | Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand | ||||||
![]() | DNA gyrase subunit B | ||||||
![]() | ISOMERASE/ISOMERASE INHIBITOR / DNA gyrase / GyrB / ligand / structure-based design / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
![]() | Zhang, J. / Yang, Q. / Cross, J.B. / Romero, J.A.C. / Ryan, M.D. / Lippa, B. / Dolle, R.E. / Andersen, O.A. / Barker, J. / Cheng, R.K. ...Zhang, J. / Yang, Q. / Cross, J.B. / Romero, J.A.C. / Ryan, M.D. / Lippa, B. / Dolle, R.E. / Andersen, O.A. / Barker, J. / Cheng, R.K. / Kahmann, J. / Felicetti, B. / Wood, M. / Scheich, C. | ||||||
![]() | ![]() Title: Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors. Authors: Zhang, J. / Yang, Q. / Cross, J.B. / Romero, J.A. / Poutsiaka, K.M. / Epie, F. / Bevan, D. / Wang, B. / Zhang, Y. / Chavan, A. / Zhang, X. / Moy, T. / Daniel, A. / Nguyen, K. / Chamberlain, ...Authors: Zhang, J. / Yang, Q. / Cross, J.B. / Romero, J.A. / Poutsiaka, K.M. / Epie, F. / Bevan, D. / Wang, B. / Zhang, Y. / Chavan, A. / Zhang, X. / Moy, T. / Daniel, A. / Nguyen, K. / Chamberlain, B. / Carter, N. / Shotwell, J. / Silverman, J. / Metcalf, C.A. / Ryan, D. / Lippa, B. / Dolle, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.1 KB | Display | ![]() |
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PDB format | ![]() | 147.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 945.3 KB | Display | ![]() |
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Full document | ![]() | 957.6 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d6pC ![]() 5d6qC ![]() 1kznS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23931.602 Da / Num. of mol.: 2 Fragment: ATP binding domain, UNP residues 2-234 (delta 105-127) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MPD / ( #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.17 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 40-43% MPD_P1K_P3350, 100 mM Mops/Na-Hepes, 100 mM Divalents |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 2, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→45.19 Å / Num. obs: 55678 / % possible obs: 96.8 % / Redundancy: 2.35 % / Rmerge(I) obs: 0.044 / Χ2: 0.98 / Net I/σ(I): 11.8 / Num. measured all: 132107 / Scaling rejects: 991 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KZN Resolution: 1.55→37.78 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2101 / WRfactor Rwork: 0.1834 / FOM work R set: 0.863 / SU B: 3.257 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0833 / SU Rfree: 0.0828 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.05 Å2 / Biso mean: 23.818 Å2 / Biso min: 10.91 Å2
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Refinement step | Cycle: final / Resolution: 1.55→37.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -4.3524 Å / Origin y: -0.5347 Å / Origin z: -16.5461 Å
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