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- PDB-4uro: Crystal Structure of Staph GyraseB 24kDa in complex with Novobiocin -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uro | ||||||
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Title | Crystal Structure of Staph GyraseB 24kDa in complex with Novobiocin | ||||||
![]() | DNA GYRASE SUBUNIT B | ||||||
![]() | ISOMERASE / ANTIBIOTICS / TOPOISOMERASE IV / NATURAL PRODUCT | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Lu, J. / Patel, S. / Sharma, N. / Soisson, S. / Kishii, R. / Takei, M. / Fukuda, Y. / Lumb, K.J. / Singh, S.B. | ||||||
![]() | ![]() Title: Structures of Kibdelomycin Bound to Staphylococcus Aureus Gyrb and Pare Showed a Novel U-Shaped Binding Mode. Authors: Lu, J. / Patel, S. / Sharma, N. / Soisson, S.M. / Kishii, R. / Takei, M. / Fukuda, Y. / Lumb, K.J. / Singh, S.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.9 KB | Display | ![]() |
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PDB format | ![]() | 126.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4urlC ![]() 4urmC ![]() 4urnC ![]() 1aj6S 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25688.619 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NOV / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.09 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH8.5, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Date: Oct 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→74.24 Å / Num. obs: 26992 / % possible obs: 99.6 % / Observed criterion σ(I): 3.3 / Redundancy: 3.7 % / Biso Wilson estimate: 53.44 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.59→2.89 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AJ6 Resolution: 2.59→74.24 Å / Cor.coef. Fo:Fc: 0.9065 / Cor.coef. Fo:Fc free: 0.8635 / SU R Cruickshank DPI: 0.71 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.616 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.301 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 43.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.282 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→74.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.69 Å / Total num. of bins used: 14
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