› 6s48

X-ray diffraction
1.9Å resolution

AvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA

Released:
DOI: 10.2210/pdb6s48/pdb
PDB entry 6s48 coloured by chain, front view.
PDB entry 6s48 coloured by chain, side view.
PDB entry 6s48 coloured by chain, top view.
Source organism: Nostoc sp. PCC 7120 = FACHB-418
Primary publication:
Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation.
Kisiala M, Kowalska M, Pastor M, Korza HJ, Czapinska H, Bochtler M
Nucleic Acids Res 48 6954-6969 (2020)
PMID: 32459314

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120602 (preferred)
Entry contents:
1 distinct polypeptide molecule
5 distinct DNA molecules
Macromolecules (6 distinct):
Type II site-specific deoxyribonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 238 amino acids
Theoretical weight: 27.16 KDa
Source organism: Nostoc sp. PCC 7120 = FACHB-418
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8YYB7 (Residues: 1-1, 3-230; Coverage: 100%)
Gene name: alr0933
Sequence domains: SinI restriction endonuclease
DNA (5'-D(*GP*AP*TP*GP*GP*TP*CP*CP*TP*AP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
DNA (5'-D(*GP*TP*AP*G)-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 4 nucleotides
Theoretical weight: 1.23 KDa
DNA (5'-D(P*GP*AP*CP*CP*AP*TP*C)-3') Chains: E, I
Molecule details ›
Chains: E, I
Length: 7 nucleotides
Theoretical weight: 2.08 KDa
DNA (5'-D(*GP*AP*TP*G)-3') Chain: F
Molecule details ›
Chain: F
Length: 4 nucleotides
Theoretical weight: 1.23 KDa
DNA (5'-D(P*GP*TP*CP*CP*TP*AP*C)-3') Chain: G
Molecule details ›
Chain: G
Length: 7 nucleotides
Theoretical weight: 2.07 KDa

Ligands and Environments

5 bound ligands:
Ligand CA 5 x CA
Ligand BME 2 x BME
Ligand 1PE 1 x 1PE
Ligand PGE 1 x PGE
Ligand SER 1 x SER
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 37.129Å b: 116.21Å c: 56.774Å
α: 90° β: 102.91° γ: 90°
R-values:
R R work R free
0.178 0.176 0.217
Expression system: Escherichia coli

Quick links

Citations

1 review citation

mRNA-based therapeutics: powerful and versatile tools to combat diseases.
Qin et al. (2022)
3 other articles

1 mention without citation

Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation.
Kisiala et al. (2020)