› 3vw4

X-ray diffraction
2.7Å resolution

Crystal structure of the DNA-binding domain of ColE2-P9 Rep in complex with the replication origin

Released:
DOI: 10.2210/pdb3vw4/pdb
PDB entry 3vw4 coloured by chain, front view.
PDB entry 3vw4 coloured by chain, side view.
PDB entry 3vw4 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural basis for replication origin unwinding by an initiator primase of plasmid ColE2-P9: duplex DNA unwinding by a single protein.
Itou H, Yagura M, Shirakihara Y, Itoh T
J Biol Chem 290 3601-11 (2015)
PMID: 25538245

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117062 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Primase C-terminal 1 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 128 amino acids
Theoretical weight: 14.73 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06B24 (Residues: 175-294; Coverage: 40%)
Gene name: rep
Structure domains:
DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 23 nucleotides
Theoretical weight: 7.06 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 23 nucleotides
Theoretical weight: 7.06 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P212121
Unit cell:
a: 47.662Å b: 61.824Å c: 273.508Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.26 0.22 0.262
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Replisome Assembly at Bacterial Chromosomes and Iteron Plasmids.
Wegrzyn et al. (2016)
2 other articles

2 mentions without citation

Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA.
Baek et al. (2024)
1 more