› 1ryr

X-ray diffraction
2.28Å resolution

REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION

Released:
DOI: 10.2210/pdb1ryr/pdb
PDB entry 1ryr coloured by chain, front view.
PDB entry 1ryr coloured by chain, side view.
PDB entry 1ryr coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Primary publication:
Replication of a cis-syn thymine dimer at atomic resolution.
Ling H, Boudsocq F, Plosky BS, Woodgate R, Yang W
Nature 424 1083-7 (2003)
PMID: 12904819

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114552 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided
5'-D(*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.76 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 2 x CA
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21212
Unit cell:
a: 98.519Å b: 101.556Å c: 52.246Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.281 0.253 0.281
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

23 review citations

Mechanisms of DNA damage, repair, and mutagenesis.
Chatterjee et al. (2017)
22 more

3 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
2 more