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Open data
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Basic information
Entry | Database: PDB / ID: 6kys | ||||||
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Title | The structure of the M. tb toxin MazF-mt1 | ||||||
![]() | Endoribonuclease MazF9 | ||||||
![]() | TOXIN / RNA endonlease / protein engineering | ||||||
Function / homology | ![]() modulation by symbiont of host process / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xie, W. / Chen, R. / Zhou, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conserved Conformational Changes in the Regulation ofMycobacterium tuberculosisMazEF-mt1. Authors: Chen, R. / Zhou, J. / Sun, R. / Du, C. / Xie, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.4 KB | Display | ![]() |
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PDB format | ![]() | 43.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kytC ![]() 6l29C ![]() 6l2aC ![]() 5hjzS 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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Unit cell |
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Components
#1: Protein | Mass: 13270.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H37Rv / Gene: mazF9, mazF-mt1, Rv2801c / Production host: ![]() ![]() References: UniProt: P71650, Hydrolases; Acting on ester bonds #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 3350, 0.1 M NaOAc pH 5.0, and 0.1 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: May 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→22.46 Å / Num. obs: 12032 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 11.7643466651 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.25 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1728 / CC1/2: 0.669 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HJZ Resolution: 2.20041403544→22.46 Å / SU ML: 0.29594408584 / Cross valid method: FREE R-VALUE / σ(F): 0.104864264202 / Phase error: 26.4034888733
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.9374750704 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20041403544→22.46 Å
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Refine LS restraints |
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LS refinement shell |
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