2HJV | pdb_00002hjv

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

• PDB DOI: https://doi.org/10.2210/pdb2HJV/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-07-02 Released: 2006-12-12 
• Deposition Author(s): McKay, D.B., Caruthers, J.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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 Struct Biol Cryst Commun 62: 1191-1195

• PubMed: 17142894 
• DOI: https://doi.org/10.1107/S1744309106044642
• Primary Citation Related Structures: 
  2HJV


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.35 kDa 
• Atom Count: 2,696 
• Modeled Residue Count: 313 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase dbpA	A, B	163	Bacillus subtilis	Mutation(s): 1  Gene Names: dbpA EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt
Find proteins for P42305 (Bacillus subtilis (strain 168)) Explore P42305  Go to UniProtKB:  P42305

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.2	α = 90
b = 105.2	β = 90
c = 66.03	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): McKay, D.B., Caruthers, J.M.

Revision History  

• 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