Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28687.41 
• Atom Count: 1926 
• Residue Count: 255 
• Unique protein chains: 1

3DD6

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

• DOI: 10.2210/pdb3DD6/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus anthracis
• Expression System: Bacillus anthracis


• Deposited: 2008-06-05 Released: 2009-02-10 
• Deposition Author(s): Rawlings, A.E., Blagova, E.V., Levdikov, V.M., Fogg, M.J., Wilson, K.S., Wilkinson, A.J., Structural Proteomics in Europe 2 (SPINE-2)

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Experimental Data Snapshot

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

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

• PubMed: 19153445 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ribonuclease PH	A	255	Bacillus anthracis	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 86.750	α = 90.00
b = 86.750	β = 90.00
c = 179.080	γ = 120.00

Software Package:

Software Name	Purpose
MOLREP	phasing
HKL-2000	data collection
REFMAC	refinement
SCALA	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-05 
• Released Date: 2009-02-10 
• Deposition Author(s): Rawlings, A.E., Blagova, E.V., Levdikov, V.M., Fogg, M.J., Wilson, K.S., Wilkinson, A.J., Structural Proteomics in Europe 2 (SPINE-2)

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