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- PDB-9foy: Ternary complex of a Mycobacterium tuberculosis DNA gyrase core f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9foy | |||||||||
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Title | Ternary complex of a Mycobacterium tuberculosis DNA gyrase core fusion with DNA and the inhibitor AMK32b | |||||||||
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![]() | ISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR / FUSION PROTEIN | |||||||||
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 / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion 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 / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kokot, M. / Hrast, M. / Feng, L. / Mitchenall, L.A. / Lawson, D.M. / Maxwell, A. / Minovski, N. / Anderluh, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Unraveling the Mycobacterium tuberculosis DNA gyrase-DNA-NBTI complex Authors: Kokot, M. / Hrast, M. / Feng, L. / Mitchenall, L.A. / Lawson, D.M. / Maxwell, A. / Minovski, N. / Anderluh, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 314.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 862.7 KB | Display | ![]() |
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Full document | ![]() | 880.5 KB | Display | |
Data in XML | ![]() | 49 KB | Display | |
Data in CIF | ![]() | 67.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 84383.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Fusion of C-terminal domain of GyrB (residues 426-675; UniProtKB entry P9WG45) to the N-terminal domain of GyrA (residues 2-500; UniProtKB entry P9WG47). In the coordinate file the fusion is ...Details: Fusion of C-terminal domain of GyrB (residues 426-675; UniProtKB entry P9WG45) to the N-terminal domain of GyrA (residues 2-500; UniProtKB entry P9WG47). In the coordinate file the fusion is treated as a single polypeptide chain. For the GyrB component, the numbering is relative to the full-length wild-type sequence, and for the GyrA component, the sequence numbering is advanced by 1000. Short non-native sequences SNA and IGSG are appended to the N- and C-termini of the fusion, respectively. There are two fusion polypeptides in the asymmetric unit corresponding to the biologically relevant assembly. Source: (gene. exp.) ![]() Gene: gyrB, Rv0005, MTCY10H4.03, gyrA, Rv0006, MTCY10H4.04 / Plasmid: PET-28B / Production host: ![]() ![]() References: UniProt: P9WG45, UniProt: P9WG47, DNA topoisomerase (ATP-hydrolysing) #2: DNA chain | Mass: 2451.630 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PET-28B / Production host: ![]() ![]() #3: DNA chain | Mass: 3638.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-A1ID8 / ( | Mass: 506.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26BrF2N3O2 / Feature type: SUBJECT OF INVESTIGATION #5: Chemical | ChemComp-A1ID9 / ( | Mass: 506.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26BrF2N3O2 / Feature type: SUBJECT OF INVESTIGATION Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.9 % / Description: NULL |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→69.23 Å / Num. obs: 50035 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.959 / Rmerge(I) obs: 0.414 / Rpim(I) all: 0.167 / Rrim(I) all: 0.447 / Χ2: 0.93 / Net I/σ(I): 4.9 / Num. measured all: 355596 |
Reflection shell | Resolution: 2.8→2.89 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.731 / Num. measured all: 31268 / Num. unique obs: 4567 / CC1/2: 0.414 / Rpim(I) all: 0.715 / Rrim(I) all: 1.875 / Χ2: 0.49 / Net I/σ(I) obs: 0.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.024 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→69.23 Å
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