› 3uld

X-ray diffraction
1.6Å resolution

High resolution structure of DNA/RNA hybrid in complex with RNase H catalytic domain D132N mutant

Released:
DOI: 10.2210/pdb3uld/pdb
PDB entry 3uld coloured by chain, front view.
PDB entry 3uld coloured by chain, side view.
PDB entry 3uld coloured by chain, top view.
Source organism: Halalkalibacterium halodurans
Entry authors: Gan JH, Abdur R, Huang Z

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116993 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Alkalihalobacillus halodurans
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q9KEI9 (Residues: 59-196; Coverage: 70%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*AP*TP*GP*TP*CP*(PGN))-3') Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.9 KDa
Source organism: Halalkalibacterium halodurans
Expression system: Not provided
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.88 KDa
Source organism: Halalkalibacterium halodurans
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 4 x MG
1 modified residue:
Ligand PGN 1 x PGN

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: C2
Unit cell:
a: 81.301Å b: 37.672Å c: 62.378Å
α: 90° β: 96.76° γ: 90°
R-values:
R R work R free
0.196 0.194 0.235
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

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