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- PDB-6m1s: The DNA Gyrase B ATP binding domain of PSEUDOMONAS AERUGINOSA in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m1s | ||||||
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Title | The DNA Gyrase B ATP binding domain of PSEUDOMONAS AERUGINOSA in complex with compound 12o | ||||||
![]() | DNA gyrase subunit B | ||||||
![]() | ISOMERASE / DNA GYRASE / TOPOISOMERASE / ATPASE DOMAIN | ||||||
Function / homology | ![]() DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, Z.H. / Zhou, Z. | ||||||
![]() | ![]() Title: Discovery of Pyrido[2,3-b]indole Derivatives with Gram-Negative Activity Targeting Both DNA Gyrase and Topoisomerase IV. Authors: Hu, Y. / Shi, H. / Zhou, M. / Ren, Q. / Zhu, W. / Zhang, W. / Zhang, Z. / Zhou, C. / Liu, Y. / Ding, X. / Shen, H.C. / Yan, S.F. / Dey, F. / Wu, W. / Zhai, G. / Zhou, Z. / Xu, Z. / Ji, Y. / ...Authors: Hu, Y. / Shi, H. / Zhou, M. / Ren, Q. / Zhu, W. / Zhang, W. / Zhang, Z. / Zhou, C. / Liu, Y. / Ding, X. / Shen, H.C. / Yan, S.F. / Dey, F. / Wu, W. / Zhai, G. / Zhou, Z. / Xu, Z. / Ji, Y. / Lv, H. / Jiang, T. / Wang, W. / Xu, Y. / Vercruysse, M. / Yao, X. / Mao, Y. / Yu, X. / Bradley, K. / Tan, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.9 KB | Display | ![]() |
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PDB format | ![]() | 133.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 990.9 KB | Display | ![]() |
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Full document | ![]() | 998.1 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m1jC ![]() 4kfgS S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 23939.787 Da / Num. of mol.: 2 / Fragment: ATP binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: gyrB, PA0004 / Production host: ![]() ![]() References: UniProt: Q9I7C2, DNA topoisomerase (ATP-hydrolysing) #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 38.00%w/v PEG3350, 200.00mM LiSO4, 100.00mM Sodium citrate (pH 5.6) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.254→31.074 Å / Num. obs: 21976 / % possible obs: 98.95 % / Redundancy: 4.6 % / Biso Wilson estimate: 32.43 Å2 / Rpim(I) all: 0.061 / Net I/σ(I): 13.45 |
Reflection shell | Resolution: 2.254→2.29 Å / Num. unique obs: 1054 / CC1/2: 0.728 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KFG Resolution: 2.254→31.074 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.37 Å2 / Biso mean: 43.537 Å2 / Biso min: 16.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.254→31.074 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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