3DD6

Crystal structure of Rph, an exoribonuclease from Bacillus anthracis at 1.7 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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This is version 1.2 of the entry. See complete history


Literature

The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 A resolution.

Rawlings, A.E.Blagova, E.V.Levdikov, V.M.Fogg, M.J.Wilson, K.S.Wilkinson, A.J.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 2-7

  • DOI: 10.1107/S1744309108041511
  • Primary Citation of Related Structures:  
    3DD6

  • PubMed Abstract: 
  • Maturation of tRNA precursors into functional tRNA molecules requires trimming of the primary transcript at both the 5' and 3' ends. Cleavage of nucleotides from the 3' stem of tRNA precursors, releasing nucleotide diphosphates, is accomplished in Bacillus by a phosphate-dependent exoribonuclease, Rph ...

    Maturation of tRNA precursors into functional tRNA molecules requires trimming of the primary transcript at both the 5' and 3' ends. Cleavage of nucleotides from the 3' stem of tRNA precursors, releasing nucleotide diphosphates, is accomplished in Bacillus by a phosphate-dependent exoribonuclease, Rph. The crystal structure of this enzyme from B. anthracis has been solved by molecular replacement to a resolution of 1.7 A and refined to an R factor of 19.3%. There is one molecule in the asymmetric unit; the crystal packing reveals the assembly of the protein into a hexamer arranged as a trimer of dimers. The structure shows two sulfate ions bound in the active-site pocket, probably mimicking the phosphate substrate and the phosphate of the 3'-terminal nucleotide of the tRNA precursor. Three other bound sulfate ions point to likely RNA-binding sites.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, The University of York, England.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease PHA255Bacillus anthracisMutation(s): 0 
Gene Names: rphBA_4715GBAA_4715BAS4377
EC: 2.7.7.56
UniProt
Find proteins for Q81LA9 (Bacillus anthracis)
Explore Q81LA9 
Go to UniProtKB:  Q81LA9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81LA9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.75α = 90
b = 86.75β = 90
c = 179.08γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-07-18
    Changes: Advisory, Data collection, Database references, Other, Structure summary