› 6vtb

X-ray diffraction
1.55Å resolution

Naegleria gruberi RNA ligase K326A mutant with ATP and Mn

Released:
DOI: 10.2210/pdb6vtb/pdb
PDB 6vtb coloured by chain and viewed from the front.
PDB 6vtb coloured by chain and viewed from the side.
PDB 6vtb coloured by chain and viewed from the top.
Source organism: Naegleria gruberi
Primary publication:
Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Unciuleac MC, Goldgur Y, Shuman S
Nucleic Acids Res 48 5603-5615 (2020)
PMID: 32315072

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA_ligase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 340 amino acids
Theoretical weight: 38.6 KDa
Source organism: Naegleria gruberi
Expression system: Escherichia coli
UniProt:
  • Canonical: D2W2Z5 (Residues: 1-339; Coverage: 100%)
Gene name: NAEGRDRAFT_82186
Sequence domains: RNA ligase

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand MN 3 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 53.031Å b: 64.221Å c: 101.888Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.163 0.195
Expression system: Escherichia coli

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