+Open data
-Basic information
Entry | Database: PDB / ID: 6l2a | ||||||
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Title | A mutant form of M. tb toxin MazEF-mt1 | ||||||
Components | mRNA interferase | ||||||
Keywords | TOXIN / RNA endonlease / protein engineering | ||||||
Function / homology | Function and homology information modulation by symbiont of host process / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.90044665179 Å | ||||||
Authors | Xie, W. / Chen, R. / Zhou, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l2a.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l2a.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 6l2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/6l2a ftp://data.pdbj.org/pub/pdb/validation_reports/l2/6l2a | HTTPS FTP |
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-Related structure data
Related structure data | 6kysSC 6kytC 6l29C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12997.886 Da / Num. of mol.: 1 / Mutation: D11S,P14A,S18A,D13G,E89A,R90A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mazF9 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0E7Y7J2, UniProt: P71650*PLUS, Hydrolases; Acting on ester bonds |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% poly (ethylene glycol) 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: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Sep 25, 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: 1.9→21.9 Å / Num. obs: 7614 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 21.7376684597 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1086 / CC1/2: 0.669 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KYS Resolution: 1.90044665179→20.5652061793 Å / SU ML: 0.13023928667 / Cross valid method: FREE R-VALUE / σ(F): 1.33792440413 / Phase error: 24.859918438
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5825143967 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.90044665179→20.5652061793 Å
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Refine LS restraints |
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LS refinement shell |
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