3ULD

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

RNA/DNA hybrid in complex with RNase H catalytic domain mutant D132N

Gan, J.H.Abdur, R.Huang, Z.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H
A
142Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Gene Names: rnhA
EC: 3.1.26.4
Find proteins for Q9KEI9 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KEI9
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')B6N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*GP*TP*CP*(PGN))-3')C6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PGN
Query on PGN
C
DNA LINKINGC10 H15 N5 O10 P2DG
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
Unit Cell:
Length (Å)Angle (°)
a = 81.301α = 90.00
b = 37.672β = 96.76
c = 62.378γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description