2Q4J

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.863 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.171 

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: 

  • 1Z90 - determined by Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)  

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:  
    2Q52, 2Q51, 2Q50, 2Q4Z, 2Q4Y, 2Q4X, 2Q4V, 2Q4U, 2Q4T, 2Q4S, 2Q4R, 2Q4Q, 2Q4P, 2Q4O, 2Q4N, 2Q4M, 2Q4L, 2Q4K, 2Q4I, 2Q4H, 2Q4F, 2Q4E, 2Q4D, 2Q4C, 2Q4B, 2Q49, 2Q4A, 2Q48, 2Q47, 2Q46, 2Q45, 2Q44, 2Q43, 2Q42, 2Q41, 2Q40, 2Q3W, 2Q3V, 2Q3U, 2Q3T, 2Q3S, 2Q3R, 2Q3Q, 2Q3P, 2Q3O, 2Q3M
  • Also Cited By: 2Q53, 2Q4W, 2Q4G

  • 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.

    Related Citations: 
    • Structure and Dynamics of UDP-Glucose Pyrophosphorylase from Arabidopsis thaliana with Bound UDP-Glucose and UTP.
      McCoy, J.G.,Bitto, E.,Bingman, C.A.,Wesenberg, G.E.,Bannen, R.M.,Kondrashov, D.A.,Phillips Jr., G.N.
      (2007) J.Mol.Biol. 366: 830

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable UTP-glucose-1-phosphate uridylyltransferase 2
A, B
469Arabidopsis thalianaMutation(s): 0 
Gene Names: UGP2
EC: 2.7.7.9
Find proteins for Q9M9P3 (Arabidopsis thaliana)
Go to Gene View: UGP2
Go to UniProtKB:  Q9M9P3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.863 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 188.680α = 90.00
b = 58.863β = 100.40
c = 89.862γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2007-09-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-08-10
    Type: Other