PDBsum entry 2qvw

Go to PDB code: 
protein metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
732 a.a.
_MN ×39
PDB id:
Name: Hydrolase
Title: Structure of giardia dicer refined against twinned data
Structure: Glp_546_48378_50642. Chain: a, b, c, d. Engineered: yes
Source: Giardia intestinalis. Organism_taxid: 5741. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
3.00Å     R-factor:   0.221     R-free:   0.263
Authors: J.A.Doudna,I.J Macrae
Key ref:
I.J.Macrae and J.A.Doudna (2007). An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer. Acta Crystallogr D Biol Crystallogr, 63, 993-999. PubMed id: 17704568 DOI: 10.1107/S0907444907036128
09-Aug-07     Release date:   25-Sep-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
A8BQJ3  (DCL_GIAIC) -  Endoribonuclease Dicer-like
754 a.a.
732 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   6 terms 
  Biochemical function     nucleotide binding     7 terms  


DOI no: 10.1107/S0907444907036128 Acta Crystallogr D Biol Crystallogr 63:993-999 (2007)
PubMed id: 17704568  
An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer.
I.J.Macrae, J.A.Doudna.
The crystal structure of the enzyme Dicer from Giardia intestinalis was solved to 3.3 A resolution by MAD using crystals belonging to space group P2(1)2(1)2 [Macrae et al. (2006), Science, 311, 195-198]. These crystals were derived from crystals that diffracted X-rays to 3.0 A resolution but were refractory to structure determination because they were twinned. It is shown here that the original Dicer crystals represent an unusual case of perfect pseudo-merohedral twinning of orthorhombic crystals. Before the twinning problem was overcome, it was possible to calculate a low-resolution electron-density map in space group P4(1) that was used to build a partial molecular model. Experimental phases were sufficient to identify heavy-atom sites that indicated space-group inconsistency, leading to identification of the true space group. This information guided the search for different crystallization conditions that yielded untwinned crystals and ultimately a fully interpretable electron-density map.
  Selected figure(s)  
Figure 5.
Figure 5 Electron-density maps (2F[o] - F[c]) contoured at 1 calculated from untwinned (left) and twinned data sets (right). Maps from twinned data contained more features, but were less reliable than those from untwinned data.
Figure 6.
Figure 6 Intermolecular contacts between Dicer molecules in the P2[1]2[1]2 lattice. The four molecules in the asymmetric unit are colored green, yellow, blue and white, respectively. Red hatched density represents a 5 peak observed by anomalous difference Fourier analysis of diffraction data measured at the Mn absorption edge.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 993-999) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19836333 P.W.Lau, C.S.Potter, B.Carragher, and I.J.MacRae (2009).
Structure of the human Dicer-TRBP complex by electron microscopy.
  Structure, 17, 1326-1332.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.