› 3zda

X-ray diffraction
1.5Å resolution

Structure of E. coli ExoIX in complex with a fragment of the Flap1 DNA oligonucleotide, potassium and magnesium

Released:
DOI: 10.2210/pdb3zda/pdb
PDB entry 3zda coloured by chain, front view.
PDB entry 3zda coloured by chain, side view.
PDB entry 3zda coloured by chain, top view.
Source organisms:
Primary publication:
The structure of Escherichia coli ExoIX--implications for DNA binding and catalysis in flap endonucleases.
Anstey-Gilbert CS, Hemsworth GR, Flemming CS, Hodskinson MR, Zhang J, Sedelnikova SE, Stillman TJ, Sayers JR, Artymiuk PJ
Nucleic Acids Res 41 8357-67 (2013)
PMID: 23821668

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117111 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Flap endonuclease Xni Chain: A
Molecule details ›
Chain: A
Length: 251 amino acids
Theoretical weight: 28.2 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8X6R9 (Residues: 1-251; Coverage: 100%)
Gene names: ECs3658, Z4115, xni, ygdG
Sequence domains:
Structure domains:
5'-D(*GP*CP*GP*CP)-3' Chain: B
Molecule details ›
Chain: B
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*AP*GP*CP*GP*CP)-3' Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.82 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand K 1 x K
Ligand MG 1 x MG
Ligand PIV 1 x PIV
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21212
Unit cell:
a: 66.203Å b: 154.82Å c: 34.473Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.211 0.235
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 citation in other articles

Comprehensive classification of the PIN domain-like superfamily.
Matelska et al. (2017)
5 more

2 mentions without citation

Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
Opron et al. (2016)
1 more