› 5d23

X-ray diffraction
1.95Å resolution

The crystal structure of STPR from Bombyx mori in complex with 13-bp DNA derived from the +290 site of fibroin gene

Released:
DOI: 10.2210/pdb5d23/pdb
PDB entry 5d23 coloured by chain, front view.
PDB entry 5d23 coloured by chain, side view.
PDB entry 5d23 coloured by chain, top view.
Source organisms:
Primary publication:
Structures of an all-α protein running along the DNA major groove.
Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X, Wu Q, Chen Y, Zhou CZ
OpenAccess logo Nucleic Acids Res 44 3936-45 (2016)
PMID: 26939889

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118523 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
STPR domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 102 amino acids
Theoretical weight: 12.05 KDa
Source organism: Bombyx mori
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5FBS0 (Residues: 99-193; Coverage: 44%)
Gene names: 692516, fmbp-1
Sequence domains: STPRs (score and three amino acid peptide repeats)
DNA (26-MER) Chain: B
Molecule details ›
Chain: B
Length: 26 nucleotides
Theoretical weight: 7.98 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 5 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: R32
Unit cell:
a: 123.18Å b: 123.18Å c: 73.574Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.205 0.232
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 citation in other articles

The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end.
Kosek et al. (2021)
2 more

1 mention without citation

Prediction of the secondary structure of short DNA aptamers.
Afanasyeva et al. (2019)