› 7ec3

X-ray diffraction
2.5Å resolution

Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide)

Released:
DOI: 10.2210/pdb7ec3/pdb
PDB entry 7ec3 coloured by chain, front view.
PDB entry 7ec3 coloured by chain, side view.
PDB entry 7ec3 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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-168204 (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: 59.63 KDa
Source organism: Staphylococcus aureus subsp. aureus USA300
Expression system: Escherichia coli
UniProt:
  • Canonical: Q2G0L2 (Residues: 1-496; Coverage: 100%)
Gene name: SAOUHSC_00548
Sequence domains: Glycosyl transferases group 1
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE Chains: D, G
Molecule details ›
Chains: D, G
Length: 8 amino acids
Theoretical weight: 827 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand UDP 2 x UDP
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P212121
Unit cell:
a: 70.201Å b: 130.568Å c: 189.854Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.24
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)