› 5hml

X-ray diffraction
1.48Å resolution

Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions

Released:
DOI: 10.2210/pdb5hml/pdb
PDB entry 5hml coloured by chain, front view.
PDB entry 5hml coloured by chain, side view.
PDB entry 5hml coloured by chain, top view.
Source organism: Escherichia virus T5
Primary publication:
Direct observation of DNA threading in flap endonuclease complexes.
AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ
Nat Struct Mol Biol 23 640-6 (2016)
PMID: 27273516

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138947 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Flap endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 272 amino acids
Theoretical weight: 31.28 KDa
Source organism: Escherichia virus T5
Expression system: Escherichia coli
UniProt:
  • Canonical: P06229 (Residues: 20-291; Coverage: 94%)
Gene names: D15, T5.130, T5p128, exo5
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand MG 3 x MG
Ligand CL 12 x CL
Ligand EDO 2 x EDO
Ligand B3P 1 x B3P
Ligand IOD 2 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P1
Unit cell:
a: 47.38Å b: 58.38Å c: 59.72Å
α: 66.53° β: 79.48° γ: 73.71°
R-values:
R R work R free
0.143 0.141 0.196
Expression system: Escherichia coli

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Citations

1 review citation

The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria.
McLean et al. (2022)
21 other articles

1 mention without citation

Direct observation of DNA threading in flap endonuclease complexes.
AlMalki et al. (2016)