› 5wzf

X-ray diffraction
1.75Å resolution

Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin

Released:
DOI: 10.2210/pdb5wzf/pdb
PDB entry 5wzf coloured by chain, front view.
PDB entry 5wzf coloured by chain, side view.
PDB entry 5wzf coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Crystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin-antitoxin assembly.
Deep A, Kaundal S, Agarwal S, Singh R, Thakur KG
FEBS J 284 4066-4082 (2017)
PMID: 28986943

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161140 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
23S rRNA-specific endonuclease VapC20 Chain: A
Molecule details ›
Chain: A
Length: 144 amino acids
Theoretical weight: 16.07 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P95004 (Residues: 2-131; Coverage: 99%)
Gene names: Rv2549c, vapC20
Sequence domains: PIN domain
23S rRNA-specific endonuclease VapC20 Chain: B
Molecule details ›
Chain: B
Length: 144 amino acids
Theoretical weight: 16.09 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P95004 (Residues: 2-131; Coverage: 99%)
Gene names: Rv2549c, vapC20
Sequence domains: PIN domain

Ligands and Environments

No bound ligands
1 modified residue:
Ligand CSO 1 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 48.81Å b: 59.14Å c: 79.29Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.198
Expression system: Escherichia coli

Quick links

Citations

10 citation in other articles

System-Wide Analysis Unravels the Differential Regulation and In Vivo Essentiality of Virulence-Associated Proteins B and C Toxin-Antitoxin Systems of Mycobacterium tuberculosis.
Agarwal et al. (2018)
9 more

2 mentions without citation

A Systematic Overview of Type II and III Toxin-Antitoxin Systems with a Focus on Druggability.
Kang et al. (2018)
1 more