› 5jjv

X-ray diffraction
2.4Å resolution

Crystal structure of XerH site-specific recombinase bound to palindromic difH substrate: post-cleavage complex

Released:
DOI: 10.2210/pdb5jjv/pdb
Model geometry
Fit model/data
PDB entry 5jjv coloured by chain, front view.
PDB entry 5jjv coloured by chain, side view.
PDB entry 5jjv coloured by chain, top view.
Source organism: Helicobacter pylori 26695
Primary publication:
Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.
Bebel A, Karaca E, Kumar B, Stark WM, Barabas O
OpenAccess logo Elife 5 (2016)
PMID: 28009253

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118871 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Tyrosine recombinase XerH Chains: A, B
Molecule details ›
Chains: A, B
Length: 363 amino acids
Theoretical weight: 42 KDa
Source organism: Helicobacter pylori 26695
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O25386 (Residues: 1-362; Coverage: 100%)
Gene names: HP_0675, xerH
Sequence domains:
DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 4 KDa
Source organism: Helicobacter pylori 26695
Expression system: Escherichia coli
DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3') Chains: D, F

Ligands and Environments

2 bound ligands:
Ligand GOL 9 x GOL
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID29
Spacegroup: I222
Unit cell:
a: 86.38Å b: 115.22Å c: 235.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.195 0.22
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

2 review citations

Xer Site Specific Recombination: Double and Single Recombinase Systems.
Castillo et al. (2017)
1 more

2 mentions without citation

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.
Bebel et al. (2016)
1 more