PDBsum entry: 2qvw

Hydrolase

PDB id: 2qvw

Contents

Protein chains

732 a.a.

Metals

_MN ×39

PDB id:

2qvw

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.

Resolution:

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

Date:

09-Aug-07 Release date: 25-Sep-07

Protein chains

A8BQJ3  (DCL_GIAIC) -  Endoribonuclease Dicer-like

Seq: 754 a.a.

Struc: 732 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: RNA processing (3 terms)
• Biochemical function: nucleotide binding (8 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.

ABSTRACT

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.