› 3jy1

X-ray diffraction
1.75Å resolution

Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site (across from C)

Released:
DOI: 10.2210/pdb3jy1/pdb
PDB entry 3jy1 coloured by chain, front view.
PDB entry 3jy1 coloured by chain, side view.
PDB entry 3jy1 coloured by chain, top view.
Source organism: Bacillus cereus ATCC 10987
Primary publication:
An unprecedented nucleic acid capture mechanism for excision of DNA damage.
Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF
Nature 468 406-11 (2010)
PMID: 20927102

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116459 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA alkylation repair protein Chain: A
Molecule details ›
Chain: A
Length: 226 amino acids
Theoretical weight: 27.07 KDa
Source organism: Bacillus cereus ATCC 10987
Expression system: Escherichia coli
UniProt:
  • Canonical: Q816E8 (Residues: 1-225; Coverage: 95%)
Gene name: BC_4913
Sequence domains: DNA alkylation repair enzyme
Structure domains: Leucine-rich Repeat Variant
DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 2.98 KDa
Source organism: Bacillus cereus ATCC 10987
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 2.96 KDa
Source organism: Bacillus cereus ATCC 10987
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 52.125Å b: 57.493Å c: 54.069Å
α: 90° β: 101.67° γ: 90°
R-values:
R R work R free
0.209 0.183 0.204
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

ATR signalling: more than meeting at the fork.
Nam et al. (2011)
7 more

2 mentions without citation

Recent advances in the structural mechanisms of DNA glycosylases.
Brooks et al. (2013)
1 more