› 5xma

X-ray diffraction
3.8Å resolution

Crystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group

Released:
DOI: 10.2210/pdb5xma/pdb
PDB entry 5xma coloured by chain, front view.
PDB entry 5xma coloured by chain, side view.
PDB entry 5xma coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of an RNA-cleaving DNAzyme.
Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L, Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J, Huang Z, Ma J, Gan J
Nat Commun 8 2006 (2017)
PMID: 29222499

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113200 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
Repair DNA polymerase X Chains: A, B
Molecule details ›
Chains: A, B
Length: 177 amino acids
Theoretical weight: 20.55 KDa
Source organism: African swine fever virus BA71V
Expression system: Escherichia coli
UniProt:
  • Canonical: P42494 (Residues: 1-174; Coverage: 100%)
Gene names: Ba71V-97, O174L
Sequence domains:
Structure domains:
DNA (36-MER) Chain: E
Molecule details ›
Chain: E
Length: 36 nucleotides
Theoretical weight: 10.99 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA/RNA (5'-D(*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*T)-R(P*G)-D(P*GP*GP*TP*GP*CP*GP*TP*TP*AP*CP*A)-3') Chain: F
Molecule details ›
Chain: F
Length: 23 nucleotides
Theoretical weight: 7.21 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P43212
Unit cell:
a: 78.846Å b: 78.846Å c: 241.677Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.26 0.258 0.285
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

DNAzymes as Activity-Based Sensors for Metal Ions: Recent Applications, Demonstrated Advantages, Current Challenges, and Future Directions.
Lake et al. (2019)
10 more

2 mentions without citation

Crystal structure of an RNA-cleaving DNAzyme.
Liu et al. (2017)
1 more