› 5jrk

X-ray diffraction
3Å resolution

Crystal Structure of the Sphingopyxin I Lasso Peptide Isopeptidase SpI-IsoP (SeMet-derived)

Released:
DOI: 10.2210/pdb5jrk/pdb
PDB entry 5jrk coloured by chain, front view.
PDB entry 5jrk coloured by chain, side view.
PDB entry 5jrk coloured by chain, top view.
Source organism: Sphingopyxis alaskensis RB2256
Primary publication:
Structure and Mechanism of the Sphingopyxin I Lasso Peptide Isopeptidase.
Fage CD, Hegemann JD, Nebel AJ, Steinbach RM, Zhu S, Linne U, Harms K, Bange G, Marahiel MA
Angew Chem Int Ed Engl 55 12717-21 (2016)
PMID: 27611791

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172851 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase S9 prolyl oligopeptidase catalytic domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 756 amino acids
Theoretical weight: 83.45 KDa
Source organism: Sphingopyxis alaskensis RB2256
Expression system: Escherichia coli B
UniProt:
  • Canonical: Q1GQ33 (Residues: 1-726; Coverage: 100%)
Gene name: Sala_2532
Sequence domains: Prolyl oligopeptidase family

Ligands and Environments

1 bound ligand:
Ligand BGC 2 x BGC
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 111.105Å b: 133.501Å c: 169.07Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.237 0.258
Expression system: Escherichia coli B

Quick links

Citations

5 review citations

Lasso Peptides: Heterologous Production and Potential Medical Application.
Cheng et al. (2020)
4 more