3DD6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.702 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


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 65: 2-7

  • DOI: 10.1107/S1744309108041511

  • 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 Ba ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease PH
A
255Bacillus anthracisMutation(s): 0 
Gene Names: rph
EC: 2.7.7.56
Find proteins for Q81LA9 (Bacillus anthracis)
Go to UniProtKB:  Q81LA9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.702 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 86.750α = 90.00
b = 86.750β = 90.00
c = 179.080γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
REFMACrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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