2Q49

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g19940


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:1XYG


Literature

Ensemble refinement of protein crystal structures: validation and application.

Levin, E.J.Kondrashov, D.A.Wesenberg, G.E.Phillips, G.N.

(2007) Structure 15: 1040-1052

  • DOI: 10.1016/j.str.2007.06.019
  • Primary Citation of Related Structures:  
    2Q3S, 2Q44, 2Q3R, 2Q43, 2Q3Q, 2Q42, 2Q3P, 2Q41, 2Q3O, 2Q40

  • PubMed Abstract: 
  • X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of repre ...

    X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable N-acetyl-gamma-glutamyl-phosphate reductaseABCD359Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g19940F6F22.3
EC: 1.2.1.38
Find proteins for Q93Z70 (Arabidopsis thaliana)
Explore Q93Z70 
Go to UniProtKB:  Q93Z70
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.597α = 90
b = 107.067β = 118.88
c = 85.754γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-08-10
    Changes: Other