› 3r8f

X-ray diffraction
3.37Å resolution

Replication initiator DnaA bound to AMPPCP and single-stranded DNA

Released:
DOI: 10.2210/pdb3r8f/pdb
PDB entry 3r8f coloured by chain, front view.
PDB entry 3r8f coloured by chain, side view.
PDB entry 3r8f coloured by chain, top view.
Source organism: Aquifex aeolicus
Primary publication:
DNA stretching by bacterial initiators promotes replication origin opening.
Duderstadt KE, Chuang K, Berger JM
Nature 478 209-13 (2011)
PMID: 21964332

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116796 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Chromosomal replication initiator protein DnaA Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 324 amino acids
Theoretical weight: 37.86 KDa
Source organism: Aquifex aeolicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O66659 (Residues: 76-399; Coverage: 81%)
Gene names: aq_322, dnaA
Sequence domains:
Structure domains:
5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3' Chain: E
Molecule details ›
Chain: E
Length: 12 nucleotides
Theoretical weight: 3.71 KDa
Source organism: Aquifex aeolicus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand ACP 4 x ACP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 99.797Å b: 114.219Å c: 201.266Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.249 0.268
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

39 review citations

Regulating DNA replication in bacteria.
Skarstad et al. (2013)
38 more

15 mentions without citation

A structural framework for replication origin opening by AAA+ initiation factors.
Duderstadt et al. (2013)
14 more