› 6jul

X-ray diffraction
2.3Å resolution

MsDpo4-DNA complex 1

Released:
DOI: 10.2210/pdb6jul/pdb
PDB entry 6jul coloured by chain, front view.
PDB entry 6jul coloured by chain, side view.
PDB entry 6jul coloured by chain, top view.
Source organisms:
Primary publication:
A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Johnson MK, Kottur J, Nair DT
Nucleic Acids Res 47 10693-10705 (2019)
PMID: 31544946

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106268 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA polymerase IV Chains: A, F
Molecule details ›
Chains: A, F
Length: 356 amino acids
Theoretical weight: 38.91 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: A0QR77 (Residues: 1-356; Coverage: 100%)
Gene names: MSMEG_1014, MSMEG_2294, dinB
Sequence domains:
DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chains: B, C, G, H
Molecule details ›
Chains: B, C, G, H
Length: 18 nucleotides
Theoretical weight: 5.51 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand 0KX 2 x 0KX
Ligand MG 4 x MG
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P212121
Unit cell:
a: 53.96Å b: 80.78Å c: 210.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.2 0.259
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA.
Nava et al. (2020)
1 more

1 mention without citation

A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Johnson et al. (2019)