› 7vfm

X-ray diffraction
2.28Å resolution

Crystal structure of SdgB (UDP and SD peptide-binding form)

Released:
DOI: 10.2210/pdb7vfm/pdb
PDB entry 7vfm coloured by chain, front view.
PDB entry 7vfm coloured by chain, side view.
PDB entry 7vfm coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins.
Kim DG, Baek I, Lee Y, Kim H, Kim JY, Bang G, Kim S, Yoon HJ, Han BW, Suh SW, Kim HS
Acta Crystallogr D Struct Biol 77 1460-1474 (2021)
PMID: 34726173

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101647 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glycosyl transferase family 1 domain-containing protein Chains: A, C
Molecule details ›
Chains: A, C
Length: 505 amino acids
Theoretical weight: 59.65 KDa
Source organism: Staphylococcus aureus subsp. aureus USA300
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0H2XGN0 (Residues: 1-496; Coverage: 100%)
Gene name: SAUSA300_0550
Sequence domains: Glycosyl transferases group 1
SER-ASP-SER-ASP Chains: E, G
Molecule details ›
Chains: E, G
Length: 5 amino acids
Theoretical weight: 537 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P21
Unit cell:
a: 42.66Å b: 206.662Å c: 65.935Å
α: 90° β: 104.83° γ: 90°
R-values:
R R work R free
0.216 0.213 0.274
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Analysis and Verification of Glycosylation Characteristics of Septic Acute Kidney Injury.
Chen et al. (2023)

1 mention without citation

Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins.
Kim et al. (2021)