› 4xpe

X-ray diffraction
1.78Å resolution

Crystal structure of 5'-CTTATGGGCCCATAAG in a host-guest complex

Released:
DOI: 10.2210/pdb4xpe/pdb
PDB entry 4xpe coloured by chain, front view.
PDB entry 4xpe coloured by chain, side view.
PDB entry 4xpe coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for a six nucleotide genetic alphabet.
Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NG
J Am Chem Soc 137 6947-55 (2015)
PMID: 25961938

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118274 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 259 amino acids
Theoretical weight: 29.35 KDa
Source organism: Moloney murine leukemia virus isolate Shinnick
Expression system: Escherichia coli
UniProt:
  • Canonical: P03355 (Residues: 683-937; Coverage: 15%)
Gene name: gag-pol
Sequence domains: Reverse transcriptase (RNA-dependent DNA polymerase)
Structure domains:
DNA (5'-D(*CP*TP*TP*AP*TP*GP*GP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 8 nucleotides
Theoretical weight: 2.46 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*CP*CP*AP*TP*AP*AP*G)-3') Chain: G
Molecule details ›
Chain: G
Length: 8 nucleotides
Theoretical weight: 2.4 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21212
Unit cell:
a: 54.623Å b: 145.385Å c: 46.801Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.216 0.237
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

Generation of Aptamers with an Expanded Chemical Repertoire.
Diafa et al. (2015)
14 more

4 mentions without citation

Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System.
Richards et al. (2017)
3 more