› 7kik

X-ray diffraction
1.73Å resolution

Wheat dwarf virus Rep domain circular permutation complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+

Released:
DOI: 10.2210/pdb7kik/pdb
PDB entry 7kik coloured by chain, front view.
PDB entry 7kik coloured by chain, side view.
PDB entry 7kik coloured by chain, top view.
Source organism: Wheat dwarf virus
Primary publication:
Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases.
Smiley AT, Tompkins KJ, Pawlak MR, Krueger AJ, Evans RL, Shi K, Aihara H, Gordon WR
OpenAccess logo mBio 14 e0258722 (2023)
PMID: 36541758

Function and Biology Details

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-511611 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Replication-associated protein Chain: A
Molecule details ›
Chain: A
Length: 137 amino acids
Theoretical weight: 15.59 KDa
Source organism: Wheat dwarf virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q67622 (Residues: 1-84; Coverage: 24%)
Gene name: C1/C2
Sequence domains: Geminivirus Rep catalytic domain
DNA (5'-D(*TP*AP*AP*TP*AP*TP*TP*AP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3 KDa
Source organism: Wheat dwarf virus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: I4
Unit cell:
a: 94.252Å b: 94.252Å c: 50.107Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.157 0.156 0.187
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 citation in other articles

Multiparametric domain insertional profiling of adeno-associated virus VP1.
Hoffmann et al. (2023)
1 more