› 5hch

X-ray diffraction
2.9Å resolution

X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair

Released:
DOI: 10.2210/pdb5hch/pdb
PDB entry 5hch coloured by chain, front view.
PDB entry 5hch coloured by chain, side view.
PDB entry 5hch coloured by chain, top view.
Source organisms:
Primary publication:
X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair.
Roethlisberger P, Istrate A, Marcaida Lopez MJ, Visini R, Stocker A, Reymond JL, Leumann CJ
Chem Commun (Camb) 52 4749-52 (2016)
PMID: 26898721

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118735 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Calcium-mediated lectin domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 114 amino acids
Theoretical weight: 11.73 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HYN5 (Residues: 2-115; Coverage: 99%)
Gene names: PA3361, lecB
Sequence domains: Fucose-binding lectin II (PA-IIL)
Structure domains: Calcium-mediated lectin
DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3') Chain: E
Molecule details ›
Chain: E
Length: 13 nucleotides
Theoretical weight: 4.05 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 2 x CA
Ligand NA 1 x NA
Ligand 61J 1 x 61J
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P6222
Unit cell:
a: 60.451Å b: 60.451Å c: 204.828Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.23 0.227 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 citation in other articles

A mixed chirality α-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Baeriswyl et al. (2021)
2 more

1 mention without citation

Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense.
Castillo et al. (2008)