3O7O

Use of synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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This is version 1.2 of the entry. See complete history


Literature

Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima.

Forse, G.J.Ram, N.Banatao, D.R.Cascio, D.Sawaya, M.R.Klock, H.E.Lesley, S.A.Yeates, T.O.

(2011) Protein Sci 20: 168-178

  • DOI: https://doi.org/10.1002/pro.550
  • Primary Citation of Related Structures:  
    3O7O

  • PubMed Abstract: 

    Protein crystallization continues to be a major bottleneck in X-ray crystallography. Previous studies suggest that symmetric proteins, such as homodimers, might crystallize more readily than monomeric proteins or asymmetric complexes. Proteins that are naturally monomeric can be made homodimeric artificially. Our approach is to create homodimeric proteins by introducing single cysteines into the protein of interest, which are then oxidized to form a disulfide bond between the two monomers. By introducing the single cysteine at different sequence positions, one can produce a variety of synthetically dimerized versions of a protein, with each construct expected to exhibit its own crystallization behavior. In earlier work, we demonstrated the potential utility of the approach using T4 lysozyme as a model system. Here we report the successful application of the method to Thermotoga maritima CelA, a thermophilic endoglucanase enzyme with low sequence identity to proteins with structures previously reported in the Protein Data Bank. This protein had resisted crystallization in its natural monomeric form, despite a broad survey of crystallization conditions. The synthetic dimerization of the CelA mutant D188C yielded well-diffracting crystals with molecules in a packing arrangement that would not have occurred with native, monomeric CelA. A 2.4 Å crystal structure was determined by single anomalous dispersion using a seleno-methionine derivatized protein. The results support the notion that synthetic symmetrization can be a useful approach for enlarging the search space for crystallizing monomeric proteins or asymmetric complexes.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoglucanase
A, B
264Thermotoga maritimaMutation(s): 1 
Gene Names: TM1524TM_1524
UniProt
Find proteins for Q9S5X8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9S5X8 
Go to UniProtKB:  Q9S5X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S5X8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.028α = 90
b = 114.028β = 90
c = 98.818γ = 120
Software Package:
Software NamePurpose
SHELXphasing
DMphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Adxvdata processing
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description