› 3wyp

X-ray diffraction
1.3Å resolution

Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution

Released:
DOI: 10.2210/pdb3wyp/pdb
PDB entry 3wyp coloured by chain, front view.
PDB entry 3wyp coloured by chain, side view.
PDB entry 3wyp coloured by chain, top view.
Source organism: Streptomyces avidinii
Primary publication:
Crystal structure of streptavidin mutant with low immunogenicity.
Kawato T, Mizohata E, Meshizuka T, Doi H, Kawamura T, Matsumura H, Yumura K, Tsumoto K, Kodama T, Inoue T, Sugiyama A
J Biosci Bioeng 119 642-7 (2015)
PMID: 25434833

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149694 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Streptavidin Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 127 amino acids
Theoretical weight: 13.28 KDa
Source organism: Streptomyces avidinii
Expression system: Escherichia coli
UniProt:
  • Canonical: P22629 (Residues: 37-163; Coverage: 80%)
Sequence domains: Avidin family
Structure domains: Avidin-like

Ligands and Environments

4 bound ligands:
Ligand BTN 2 x BTN
Ligand GOL 10 x GOL
Ligand BSO 2 x BSO
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 50.354Å b: 97.696Å c: 52.57Å
α: 90° β: 112.29° γ: 90°
R-values:
R R work R free
0.133 0.131 0.179
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Cupid and Psyche system for the diagnosis and treatment of advanced cancer.
Sugiyama et al. (2019)
1 more

1 mention without citation

Reduced background autofluorescence for cell imaging using nanodiamonds and lanthanide chelates.
Cordina et al. (2018)