› 5ecd

X-ray diffraction
1.75Å resolution

Structure of the Shigella flexneri VapC mutant D98N crystal form 1

Released:
DOI: 10.2210/pdb5ecd/pdb
PDB entry 5ecd coloured by chain, front view.
PDB entry 5ecd coloured by chain, side view.
PDB entry 5ecd coloured by chain, top view.
Source organism: Shigella flexneri
Primary publication:
Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri.
Xu K, Dedic E, Brodersen DE
Proteins 84 892-9 (2016)
PMID: 26833558

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126528 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA(fMet)-specific endonuclease VapC Chains: A, B
Molecule details ›
Chains: A, B
Length: 138 amino acids
Theoretical weight: 15.66 KDa
Source organism: Shigella flexneri
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O06662 (Residues: 2-132; Coverage: 99%)
Gene names: CP0245, mvpA, stborf2, vapC
Sequence domains: PIN domain
Structure domains: 5'-nuclease

Ligands and Environments

1 bound ligand:
Ligand EPE 2 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: R3
Unit cell:
a: 121.45Å b: 121.45Å c: 51.74Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.164 0.161 0.197
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

Structural conservation of the PIN domain active site across all domains of life.
Senissar et al. (2017)
1 more

2 mentions without citation

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)
1 more