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- PDB-8c24: ParDE1 toxin-antitoxin complex from Mycobacterium tuberculosis (r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c24 | ||||||
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Title | ParDE1 toxin-antitoxin complex from Mycobacterium tuberculosis (rv1960c-rv1959c) | ||||||
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![]() | TOXIN / Toxin-antitoxin system Gyrase inhibitor Tuberculosis | ||||||
Function / homology | ![]() modulation by symbiont of host process / detoxification / toxin sequestering activity / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beck, I.N. / Blower, T.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Toxin release by conditional remodelling of ParDE1 from Mycobacterium tuberculosis leads to gyrase inhibition. Authors: Beck, I.N. / Arrowsmith, T.J. / Grobbelaar, M.J. / Bromley, E.H.C. / Marles-Wright, J. / Blower, T.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.7 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.8 KB | Display | ![]() |
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Full document | ![]() | 469.9 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c26C ![]() 3kxeS S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 11317.714 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: parE1, Rv1959c / Production host: ![]() ![]() #2: Protein | Mass: 9254.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: parD1, Rv1960c, MTCY09F9.04 / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350 0.2 M Sodium nitrate 0.1 M Bis-tris propane pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.92 Å / Num. obs: 31537 / % possible obs: 99.57 % / Redundancy: 2 % / Biso Wilson estimate: 39.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.13 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 3147 / CC1/2: 0.669 / % possible all: 99.05 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KXE Resolution: 2.1→45.92 Å / SU ML: 0.2546 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2882 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.92 Å
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Refine LS restraints |
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LS refinement shell |
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