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- PDB-8ypj: Cyrstal structure of the MazE-mt10 Antitoxin from Mycobacterium t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ypj | ||||||
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Title | Cyrstal structure of the MazE-mt10 Antitoxin from Mycobacterium tuberculosis | ||||||
![]() | Antitoxin![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / regulation of DNA-templated transcription / ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, K.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: DNA binding reveals hidden interdomain allostery of a MazE antitoxin from Mycobacterium tuberculosis. Authors: Eun, H.J. / Lee, S.Y. / Lee, K.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.2 KB | Display | ![]() |
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PDB format | ![]() | 21 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Components
#1: Protein | ![]() Mass: 8141.198 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / | ![]() #3: 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: 2.51 Å3/Da / Density % sol: 51.01 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES (pH 6), 20% (w/v) PEG 6000, 0.2 M NH4Cl |
-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 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.91→30 Å / Num. obs: 12759 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.91→1.94 Å / Rmerge(I) obs: 0.097 / Num. unique obs: 648 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→30 Å
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Refine LS restraints |
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LS refinement shell |
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