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Yorodumi- PDB-8an5: MenAT1 toxin-antitoxin complex (rv0078a-rv0078b) from Mycobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8an5 | ||||||
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Title | MenAT1 toxin-antitoxin complex (rv0078a-rv0078b) from Mycobacterium tuberculosis H37Rv | ||||||
Components |
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Keywords | TOXIN / Toxin-antitoxin Tuberculosis Nucleotidyltransferase MenT MenAT | ||||||
Function / homology | Rv0078B-like antitoxin / Rv0078B-related antitoxin / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyltransferase superfamily / Conserved protein / Nucleotidyl transferase AbiEii/AbiGii toxin family protein Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.44 Å | ||||||
Authors | Xu, X. / Usher, B. / Gutierrez, C. / Barriot, R. / Arrowsmith, T.J. / Han, X. / Redder, P. / Neyrolles, O. / Blower, T.R. / Genevaux, P. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding. Authors: Xu, X. / Usher, B. / Gutierrez, C. / Barriot, R. / Arrowsmith, T.J. / Han, X. / Redder, P. / Neyrolles, O. / Blower, T.R. / Genevaux, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8an5.cif.gz | 268.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8an5.ent.gz | 211.8 KB | Display | PDB format |
PDBx/mmJSON format | 8an5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8an5_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 8an5_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 8an5_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 8an5_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/8an5 ftp://data.pdbj.org/pub/pdb/validation_reports/an/8an5 | HTTPS FTP |
-Related structure data
Related structure data | 8an4C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21509.369 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv0078A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7N686 #2: Protein | | Mass: 7416.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv0078B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6X8G2 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium fluoride 0.1 M Bis-Tris propane pH 6.5 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→43.68 Å / Num. obs: 82208 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 23.85 Å2 / CC1/2: 1 / Net I/σ(I): 13.07 |
Reflection shell | Resolution: 1.44→1.492 Å / Num. unique obs: 8166 / CC1/2: 0.63 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.44→43.68 Å / SU ML: 0.1947 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1716 Stereochemistry target values: GeoStd + Monomer Library + 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: 37.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→43.68 Å
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Refine LS restraints |
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LS refinement shell |
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