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

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

Starting Model: experimental
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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 Struct Biol Cryst Commun 62: 1191-1195

  • DOI: https://doi.org/10.1107/S1744309106044642
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase dbpA
A, B
163Bacillus subtilisMutation(s): 1 
Gene Names: dbpA
EC: 3.6.1
Find proteins for P42305 (Bacillus subtilis (strain 168))
Explore P42305 
Go to UniProtKB:  P42305
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42305
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.2α = 90
b = 105.2β = 90
c = 66.03γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description