› 5jqf

X-ray diffraction
0.85Å resolution

Crystal structure of the lasso peptide Sphingopyxin I (SpI)

Released:
DOI: 10.2210/pdb5jqf/pdb
PDB entry 5jqf coloured by chain, front view.
PDB entry 5jqf coloured by chain, side view.
PDB entry 5jqf 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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-103359 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sphingopyxin I Chains: A, B
Molecule details ›
Chains: A, B
Length: 21 amino acids
Theoretical weight: 2.2 KDa
Source organism: Sphingopyxis alaskensis RB2256
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A1D5B387 (Residues: 1-21; Coverage: 100%)

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P65
Unit cell:
a: 39.24Å b: 39.24Å c: 31.41Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.13 0.129 0.153
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

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

1 mention without citation

Pandonodin: A Proteobacterial Lasso Peptide with an Exceptionally Long C-Terminal Tail.
Cheung-Lee et al. (2019)