› 3gpl

X-ray diffraction
2.5Å resolution

Crystal structure of the ternary complex of RecD2 with DNA and ADPNP

Released:
DOI: 10.2210/pdb3gpl/pdb
PDB entry 3gpl coloured by chain, front view.
PDB entry 3gpl coloured by chain, side view.
PDB entry 3gpl coloured by chain, top view.
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Primary publication:
Mechanistic basis of 5'-3' translocation in SF1B helicases.
Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley DB
Cell 137 849-59 (2009)
PMID: 19490894

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116322 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
ATP-dependent RecD2 DNA helicase Chains: A, B
Molecule details ›
Chains: A, B
Length: 574 amino acids
Theoretical weight: 61.47 KDa
Source organism: Deinococcus radiodurans R1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9RT63 (Residues: 151-715; Coverage: 79%)
Gene names: DR_1902, recD2
Sequence domains:
Structure domains:
5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3' Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 8 nucleotides
Theoretical weight: 2.39 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ANP 2 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 66.12Å b: 130.36Å c: 80.05Å
α: 90° β: 107.34° γ: 90°
R-values:
R R work R free
0.232 0.232 0.273
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

18 review citations

SF1 and SF2 helicases: family matters.
Fairman-Williams et al. (2010)
17 more

9 mentions without citation

Structure and function of Pif1 helicase.
Byrd et al. (2017)
8 more