Crystal structure of quintuple Arg-to-Lys variant of T. celer L30e

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.189 

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Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values

Chan, C.H.Wilbanks, C.C.Makhatadze, G.I.Wong, K.B.

(2012) PLoS One 7: e30296-e30296

  • DOI: https://doi.org/10.1371/journal.pone.0030296
  • Primary Citation of Related Structures:  
    3N4Y, 3N4Z

  • PubMed Abstract: 

    Optimization of the surface charges is a promising strategy for increasing thermostability of proteins. Electrostatic contribution of ionizable groups to the protein stability can be estimated from the differences between the pKa values in the folded and unfolded states of a protein. Using this pKa-shift approach, we experimentally measured the electrostatic contribution of all aspartate and glutamate residues to the stability of a thermophilic ribosomal protein L30e from Thermococcus celer. The pKa values in the unfolded state were found to be similar to model compound pKas. The pKa values in both the folded and unfolded states obtained at 298 and 333 K were similar, suggesting that electrostatic contribution of ionizable groups to the protein stability were insensitive to temperature changes. The experimental pKa values for the L30e protein in the folded state were used as a benchmark to test the robustness of pKa prediction by various computational methods such as H++, MCCE, MEAD, pKD, PropKa, and UHBD. Although the predicted pKa values were affected by crystal contacts that may alter the side-chain conformation of surface charged residues, most computational methods performed well, with correlation coefficients between experimental and calculated pKa values ranging from 0.49 to 0.91 (p<0.01). The changes in protein stability derived from the experimental pKa-shift approach correlate well (r = 0.81) with those obtained from stability measurements of charge-to-alanine substituted variants of the L30e protein. Our results demonstrate that the knowledge of the pKa values in the folded state provides sufficient rationale for the redesign of protein surface charges leading to improved protein stability.

  • Organizational Affiliation

    Centre for Protein Science and Crystallography, School of Life Science, The Chinese University of Hong Kong, Hong Kong, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30e
A, B
101Thermococcus celerMutation(s): 5 
Gene Names: rpl30erpl30
Find proteins for P29160 (Thermococcus celer)
Explore P29160 
Go to UniProtKB:  P29160
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29160
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.189 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.487α = 90
b = 61.36β = 90
c = 102.767γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-01
    Changes: Database references
  • Version 1.3: 2012-06-27
    Changes: Database references
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Refinement description