› 8bbm

X-ray diffraction
1.95Å resolution

DNA binding domain of J-DNA Binding Protein 1 (JBP1)

Released:
DOI: 10.2210/pdb8bbm/pdb
Model geometry
Fit model/data
PDB entry 8bbm coloured by chain, front view.
PDB entry 8bbm coloured by chain, side view.
PDB entry 8bbm coloured by chain, top view.
Source organism: Leishmania tarentolae
Primary publication:
Distant sequence regions of JBP1 contribute to J-DNA binding.
de Vries I, Ammerlaan D, Heidebrecht T, Celie PH, Geerke DP, Joosten RP, Perrakis A
OpenAccess logo Life Sci Alliance 6 (2023)
PMID: 37328191

Function and Biology Details

Reaction catalysed: 
Thymine + 2-oxoglutarate + O(2) = 5-hydroxymethyluracil + succinate + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193613 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymine dioxygenase JBP1 Chain: A
Molecule details ›
Chain: A
Length: 170 amino acids
Theoretical weight: 20.54 KDa
Source organism: Leishmania tarentolae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9U6M1 (Residues: 392-561; Coverage: 21%)
Gene name: JBP1
Sequence domains: Thymine dioxygenase JBP1 DNA-binding domain

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 11 x MSE

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS-II BEAMLINE 17-ID-1
Spacegroup: P6122
Unit cell:
a: 68.286Å b: 68.286Å c: 185.842Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.202 0.252
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 mentions without citation

Behind Base J: The Roles of JBP1 and JBP2 on Trypanosomatids.
Assis et al. (2023)
1 more