› 4jk3

X-ray diffraction
2.5Å resolution

PylD holoenzyme (SeMet)

Released:
DOI: 10.2210/pdb4jk3/pdb
PDB entry 4jk3 coloured by chain, front view.
PDB entry 4jk3 coloured by chain, side view.
PDB entry 4jk3 coloured by chain, top view.
Source organism: Methanosarcina barkeri str. Fusaro
Primary publication:
Structure and reaction mechanism of pyrrolysine synthase (PylD).
Quitterer F, Beck P, Bacher A, Groll M
Angew Chem Int Ed Engl 52 7033-7 (2013)
PMID: 23720358

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-175176 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrrolysine synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 259 amino acids
Theoretical weight: 28.16 KDa
Source organism: Methanosarcina barkeri str. Fusaro
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q46E80 (Residues: 5-263; Coverage: 99%)
Gene names: Mbar_A0835, pylD
Sequence domains: Pyrrolysine biosynthesis protein PylD, N-terminal domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand NAD 2 x NAD
Ligand NA 2 x NA
Ligand MG 2 x MG
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21212
Unit cell:
a: 79.65Å b: 155.4Å c: 39.57Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.216 0.257
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Pyrrolysine Amber Stop-Codon Suppression: Development and Applications.
Brabham et al. (2017)
1 more