› 5fpx

X-ray diffraction
1.5Å resolution

The structure of KdgF from Yersinia enterocolitica.

Released:
DOI: 10.2210/pdb5fpx/pdb
PDB entry 5fpx coloured by chain, front view.
PDB entry 5fpx coloured by chain, side view.
PDB entry 5fpx coloured by chain, top view.
Source organism: Yersinia enterocolitica subsp. enterocolitica 8081
Primary publication:
KdgF, the missing link in the microbial metabolism of uronate sugars from pectin and alginate.
Hobbs JK, Lee SM, Robb M, Hof F, Barr C, Abe KT, Hehemann JH, McLean R, Abbott DW, Boraston AB
Proc Natl Acad Sci U S A 113 6188-93 (2016)
PMID: 27185956

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106625 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cupin type-2 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 113 amino acids
Theoretical weight: 12.83 KDa
Source organism: Yersinia enterocolitica subsp. enterocolitica 8081
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A1JMF7 (Residues: 2-110; Coverage: 99%)
Gene names: YE1889, kdgF
Sequence domains: Cupin domain
Structure domains: Jelly Rolls
PEPTIDE Chains: E, F
Molecule details ›
Chains: E, F
Length: 8 amino acids
Theoretical weight: 940 Da
Source organism: Yersinia enterocolitica subsp. enterocolitica 8081
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 39.92Å b: 73.76Å c: 83.68Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.199
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Microbial hexuronate catabolism in biotechnology.
Kuivanen et al. (2019)
5 more

2 mentions without citation

KdgF, the missing link in the microbial metabolism of uronate sugars from pectin and alginate.
Hobbs et al. (2016)
1 more