› 6fi8

X-ray diffraction
2.6Å resolution

Crystal structure of the IS608 transposase in complex with left end 29-mer DNA hairpin and a 6-mer DNA representing the intact target site: pre-cleavage target capture complex

Released:
DOI: 10.2210/pdb6fi8/pdb
PDB entry 6fi8 coloured by chain, front view.
PDB entry 6fi8 coloured by chain, side view.
PDB entry 6fi8 coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering.
Morero NR, Zuliani C, Kumar B, Bebel A, Okamoto S, Guynet C, Hickman AB, Chandler M, Dyda F, Barabas O
Nucleic Acids Res 46 4152-4163 (2018)
PMID: 29635476

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119902 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transposase IS200-like domain-containing protein Chains: A, B, G, H
Molecule details ›
Chains: A, B, G, H
Length: 159 amino acids
Theoretical weight: 18.39 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli
UniProt:
  • Canonical: Q933Z0 (Residues: 2-155; Coverage: 99%)
Gene names: B0X28_06285, B0X28_06415, B0X28_06965, B0X28_07035, B0X28_07355, B0X28_07380, B0X28_07400, B0X28_07410, B0X28_08670, B0X29_00655, B0X39_04170, BB413_07925, BB437_07715, DD756_06260, DDP35_01150, DDP42_08030, EC527_06560, EC565_08270, EPC71_00690, EPC72_02395, tnpA
Sequence domains: Transposase IS200 like
Structure domains: Transposase IS200-like
DNA 29-MER (LE29) Chains: C, D, I, J
Molecule details ›
Chains: C, D, I, J
Length: 29 nucleotides
Theoretical weight: 8.93 KDa
Source organism: Helicobacter pylori
Expression system: Not provided
DNA 6-MER (T6') Chains: E, F, K, L
Molecule details ›
Chains: E, F, K, L
Length: 6 nucleotides
Theoretical weight: 1.77 KDa
Source organism: Helicobacter pylori
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 16 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P41212
Unit cell:
a: 138.64Å b: 138.64Å c: 117.95Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.197 0.238
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Genomic landscapes of bacterial transposons and their applications in strain improvement.
Wu et al. (2022)
4 other articles

2 mentions without citation

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering.
Tompkins et al. (2021)
1 more