› 8tip

X-ray diffraction
2.79Å resolution

Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with blunt ends and 5' terminal phosphates.

Released:
DOI: 10.2210/pdb8tip/pdb
PDB entry 8tip coloured by chain, front view.
PDB entry 8tip coloured by chain, side view.
PDB entry 8tip coloured by chain, top view.
Source organisms:
Primary publication:
Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals.
Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD
ACS Nanosci Au 4 338-348 (2024)
PMID: 39430379

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-222945 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Replication initiation protein Chain: C
Molecule details ›
Chain: C
Length: 263 amino acids
Theoretical weight: 30.75 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P03856 (Residues: 1-251; Coverage: 100%)
Gene names: E, ECOK12F045, rep, repE
Sequence domains:
DNA (5'-D(A*CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*AP*CP*GP*G)-3')| Chain: A
Molecule details ›
Chain: A
Length: 32 nucleotides
Theoretical weight: 9.8 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(A*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*TP*CP*CP*GP*GP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 32 nucleotides
Theoretical weight: 9.9 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: I222
Unit cell:
a: 74.85Å b: 132.913Å c: 136.374Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.192 0.24
Expression systems:
  • Escherichia coli
  • Not provided

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