› 7vfn

X-ray diffraction
1.9Å resolution

Crystal structure of SdgB (SD peptide-binding form)

Released:
DOI: 10.2210/pdb7vfn/pdb
PDB entry 7vfn coloured by chain, front view.
PDB entry 7vfn coloured by chain, side view.
PDB entry 7vfn 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
OpenAccess logo 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

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-101648 (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
ASP-SER-ASP Chain: B
Molecule details ›
Chain: B
Length: 3 amino acids
Theoretical weight: 335 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P21
Unit cell:
a: 43.15Å b: 206.172Å c: 66.4Å
α: 90° β: 105.32° γ: 90°
R-values:
R R work R free
0.222 0.22 0.26
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)