2QVW

Structure of Giardia Dicer refined against twinned data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 D Biol Crystallogr 63: 993-999

  • DOI: https://doi.org/10.1107/S0907444907036128
  • Primary Citation of Related Structures:  
    2QVW

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLP_546_48378_50642
A, B, C, D
756Giardia intestinalisMutation(s): 0 
EC: 3.1.26.3
UniProt
Find proteins for A8BQJ3 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
Explore A8BQJ3 
Go to UniProtKB:  A8BQJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8BQJ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
E [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth B],
QA [auth D],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 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
b = 173.49β = 90
c = 155.453γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description