2QVW

Structure of Giardia Dicer refined against twinned data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer

Macrae, I.J.Doudna, J.A.

(2007) Acta Crystallogr.,Sect.D 63: 993-999

  • DOI: 10.1107/S0907444907036128

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLP_546_48378_50642
A, B, C, D
756Giardia intestinalis (strain ATCC 50803 / WB clone C6)Mutation(s): 0 
EC: 3.1.26.-
Find proteins for A8BQJ3 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
Go to UniProtKB:  A8BQJ3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 155.409α = 90.00
b = 173.490β = 90.00
c = 155.453γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
CNSphasing
HKL-2000data reduction
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary