2HJV

Structure of the second domain (residues 207-368) of the Bacillus subtilis YxiN protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN.

Caruthers, J.M.Hu, Y.McKay, D.B.

(2006) Acta Crystallogr.,Sect.F 62: 1191-1195

  • DOI: 10.1107/S1744309106044642

  • PubMed Abstract: 
  • The Bacillus subtilis RNA helicase YxiN is a modular three-domain protein. The first two domains form a conserved helicase core that couples an ATPase activity to an RNA duplex-destabilization activity, while the third domain recognizes a stem-loop o ...

    The Bacillus subtilis RNA helicase YxiN is a modular three-domain protein. The first two domains form a conserved helicase core that couples an ATPase activity to an RNA duplex-destabilization activity, while the third domain recognizes a stem-loop of 23S ribosomal RNA with high affinity and specificity. The structure of the second domain, amino-acid residues 207-368, has been solved to 1.95 A resolution, revealing a parallel alphabeta-fold. The crystallographic asymmetric unit contains two protomers; superposition shows that they differ substantially in two segments of peptide that overlap the conserved helicase sequence motifs V and VI, while the remainder of the domain is isostructural. The conformational variability of these segments suggests that induced fit is intrinsic to the recognition of ligands (ATP and RNA) and the coupling of the ATPase activity to conformational changes.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase dbpA
A, B
163Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: dbpA (deaD, yxiN)
EC: 3.6.4.13
Find proteins for P42305 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42305
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 105.200α = 90.00
b = 105.200β = 90.00
c = 66.030γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance