› 6ged

X-ray diffraction
1.79Å resolution

Adhesin domain of PrgB from Enterococcus faecalis bound to DNA

Released:
DOI: 10.2210/pdb6ged/pdb
PDB entry 6ged coloured by chain, front view.
PDB entry 6ged coloured by chain, side view.
PDB entry 6ged coloured by chain, top view.
Source organisms:
Primary publication:
PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction.
Schmitt A, Jiang K, Camacho MI, Jonna VR, Hofer A, Westerlund F, Christie PJ, Berntsson RP
Mol Microbiol 109 291-305 (2018)
PMID: 29723434

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119947 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Gram-positive cocci surface proteins LPxTG domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 315 amino acids
Theoretical weight: 34.16 KDa
Source organism: Enterococcus faecalis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q04112 (Residues: 246-558; Coverage: 24%)
Gene name: prgB
Sequence domains: Glucan-binding protein C
DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*GP*GP*GP*CP*CP*GP*CP*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 10 nucleotides
Theoretical weight: 3.01 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NA 1 x NA
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: P212121
Unit cell:
a: 32.017Å b: 93.026Å c: 99.097Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.212
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Extracellular DNA (eDNA). A Major Ubiquitous Element of the Bacterial Biofilm Architecture.
Campoccia et al. (2021)
8 more

3 mentions without citation

Polymer Adhesin Domains in Gram-Positive Cell Surface Proteins.
Järvå et al. (2020)
2 more