2Q4L

Ensemble refinement of the crystal structure of GALT-like protein from Arabidopsis thaliana At5g18200


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

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:1ZWJ


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, 2Q3M, 2Q4L, 2Q4K, 2Q4J, 2Q4I, 2Q4H, 2Q4F, 2Q4E, 2Q4T, 2Q4S, 2Q4R, 2Q4Q, 2Q52, 2Q4P, 2Q51, 2Q4O, 2Q50, 2Q4N, 2Q4M, 2Q49, 2Q3W, 2Q48, 2Q3V, 2Q47, 2Q3U, 2Q46, 2Q3T, 2Q45, 2Q4D, 2Q4C, 2Q4B, 2Q4A, 2Q4Z, 2Q4Y, 2Q4X, 2Q4V, 2Q4U

  • 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 representing structural flexibility ...

    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 Mechanism of an ADP-Glucose Phosphorylase from
      McCoy, J.G., Arabshahi, A., Bitto, E., Bingman, C.A., Ruzicka, F.J., Frey, P.A., Phillips Jr., G.N.
      (2006) Biochemistry 45: 3154

    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 galactose-1-phosphate uridyl transferaseA, B351Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g18200MRG7_16MRG7.16
EC: 2.7.7.12 (PDB Primary Data), 2.7.7 (UniProt)
UniProt
Find proteins for Q9FK51 (Arabidopsis thaliana)
Explore Q9FK51 
Go to UniProtKB:  Q9FK51
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.984α = 90
b = 95.535β = 90
c = 110.522γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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