Journal of Structural and Functional Genomics

, Volume 13, Issue 4, pp 227–232

Pitfalls in the interpretation of structural changes in mutant proteins from crystal structures

  • P. R. Pokkuluri
  • X. Yang
  • Y. Y. Londer
  • M. Schiffer

DOI: 10.1007/s10969-012-9147-1

Cite this article as:
Pokkuluri, P.R., Yang, X., Londer, Y.Y. et al. J Struct Funct Genomics (2012) 13: 227. doi:10.1007/s10969-012-9147-1


PpcA is a small protein with 71 residues that contains three covalently bound hemes. The structures of single mutants at residue 58 have shown larger deviations in another part of the protein molecule than at the site of the mutation. Closer examination of the crystal packing has revealed the origin of this unexpected structural change. The site of mutation is within Van der Waals distance from another protein molecule related by a crystallographic twofold axis within the crystal. The structural changes occurred at or near the mutation site have led to a slight adjustment of the surface residues in contact. The observed deviations between the native and the mutant molecular structures are derived from the new crystal packing even though the two crystals are essentially isomorphous. Without careful consideration of the crystal lattice a non-expert looking at only the coordinates deposited in the Protein Data Bank could draw erroneous conclusion that mutation in one part of the molecule affected the structure of the protein in a distant part of the molecule.


Crystal contacts Crystal packing effects Cytochrome c7 Geobacter sulfurreducens Single mutant structures Structural changes 



Desulfuromonas acetoxidans


Geobacter sulfurreducens


Nuclear magnetic resonance


Protein Data Bank


Periplasmic cytochrome A


Root mean square deviation

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • P. R. Pokkuluri
    • 1
  • X. Yang
    • 1
  • Y. Y. Londer
    • 1
    • 2
  • M. Schiffer
    • 1
  1. 1.Biosciences DivisionArgonne National LaboratoryLemontUSA
  2. 2.New England BiolabsIpswichUSA

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