3ULD

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

Structural Biology Knowledgebase: 3ULD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 3ULD

Classification: HYDROLASE / RNA / DNA

Total Structure Weight: 20206.28


Macromolecule Entities
Molecule Chains Length Organism Details
Ribonuclease H A 142 Bacillus halodurans EC#: 3.1.26.4 IUBMB
Fragment: catalytic domain
Mutation: D132N
Gene Name(s): rnhA BH0863
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3') B 6 synthetic
DNA (5'-D(*AP*TP*GP*TP*CP*(PGN))-3') C 6 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PGN
Query on PGN
C DNA LINKING C10 H15 N5 O10 P2 DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.194
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.30 α = 90.00
b = 37.67 β = 96.76
c = 62.38 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-11-10
  • Released Date: 2012-11-14
  • Deposition author(s): Gan, J.H., Abdur, R., Huang, Z.

Revision History

No revisions since initial release