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- PDB-5xe3: Endoribonuclease in complex with its cognate antitoxin from Mycob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xe3 | |||||||||
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Title | Endoribonuclease in complex with its cognate antitoxin from Mycobacterial species | |||||||||
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![]() | HYDROLASE/ANTITOXIN / endonuclease / HYDROLASE-ANTITOXIN complex | |||||||||
Function / homology | ![]() negative regulation of DNA topoisomerase (ATP-hydrolyzing) activity / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ahn, D.-H. / Lee, K.-Y. / Lee, S.J. / Yoon, H.J. / Kim, S.-J. / Lee, B.-J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analyses of the MazEF4 toxin-antitoxin pair in Mycobacterium tuberculosis provide evidence for a unique extracellular death factor. Authors: Ahn, D.H. / Lee, K.Y. / Lee, S.J. / Park, S.J. / Yoon, H.J. / Kim, S.J. / Lee, B.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.6 KB | Display | ![]() |
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PDB format | ![]() | 174.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
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Full document | ![]() | 477.2 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xe2C ![]() 3se5S 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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Unit cell |
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Components
#1: Protein | Mass: 11697.274 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: mazF4, mazF-mt7, Rv1495, MTCY277.17 / Production host: ![]() ![]() References: UniProt: P9WII5, Hydrolases; Acting on ester bonds #2: Protein | Mass: 9211.135 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: mazE4, mazE-mt7, Rv1494, MTCY277.16 / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.04 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7 Details: 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.0, 20% (w/v) polyethylene glycol 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 23785 / % possible obs: 95.21 % / Redundancy: 4 % / Net I/σ(I): 30.21 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SE5 Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.27 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.434 / ESU R Free: 0.274 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.57 Å2 / Biso mean: 44.244 Å2 / Biso min: 22.49 Å2
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Refinement step | Cycle: final / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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