› 1rys

X-ray diffraction
2.03Å resolution

REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION

Released:
DOI: 10.2210/pdb1rys/pdb
PDB entry 1rys coloured by chain, front view.
PDB entry 1rys coloured by chain, side view.
PDB entry 1rys 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-114553 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, B
Molecule details ›
Chains: A, B
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*AP*AP*GP*GP*AP*TP*TP*CP*A)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 4.08 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided
5'-D(*TP*CP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 18 nucleotides
Theoretical weight: 5.35 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand CA 5 x CA
Ligand NA 1 x NA
Ligand EDO 1 x EDO
Ligand ATP 2 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 98.732Å b: 102.29Å c: 106.069Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.256 0.221 0.256
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

5 mentions without citation

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