Correlation Between Protein Sequence Similarity and X-Ray Diffraction Quality in the Protein Data Bank

Author(s): Hui-Meng Lu, Da-Chuan Yin, Ya-Jing Ye, Hui-Min Luo, Li-Qiang Geng, Hai-Sheng Li, Wei-Hong Guo, Peng Shang

Journal Name: Protein & Peptide Letters

Volume 16 , Issue 1 , 2009


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Abstract:

As the most widely utilized technique to determine the 3-dimensional structure of protein molecules, X-ray crystallography can provide structure of the highest resolution among the developed techniques. The resolution obtained via X-ray crystallography is known to be influenced by many factors, such as the crystal quality, diffraction techniques, and X-ray sources, etc. In this paper, the authors found that the protein sequence could also be one of the factors. We extracted information of the resolution and the sequence of proteins from the Protein Data Bank (PDB), classified the proteins into different clusters according to the sequence similarity, and statistically analyzed the relationship between the sequence similarity and the best resolution obtained. The results showed that there was a pronounced correlation between the sequence similarity and the obtained resolution. These results indicate that protein structure itself is one variable that may affect resolution when X-ray crystallography is used.

Keywords: Protein sequence, protein crystallization, molecular structure, structural resolution, sequence similarity, X-ray crystallography

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Article Details

VOLUME: 16
ISSUE: 1
Year: 2009
Page: [50 - 55]
Pages: 6
DOI: 10.2174/092986609787049457

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