Djinovic-Carugo Kristina, Carugo Oliviero
Department of Structural and Computational Biology; Max F. Perutz Laboratories, Vienna University, Vienna Biocenter (VBC); Vienna, Austria; Department of Biochemistry; Faculty of Chemistry and Chemical Technology, University of Ljubljana; Ljubljana, Slovenia.
Department of Structural and Computational Biology; Max F. Perutz Laboratories, Vienna University, Vienna Biocenter (VBC); Vienna, Austria; Department of Chemistry; Pavia University; Pavia, Italy.
Intrinsically Disord Proteins. 2015 Oct 23;3(1):e1095697. doi: 10.1080/21690707.2015.1095697. eCollection 2015.
A large fraction of the protein crystal structures deposited in the Protein Data Bank are incomplete, since the position of one or more residues is not reported, despite these residues are part of the material that was analyzed. This may bias the use of the protein crystal structures by molecular biologists. Here we observe that in the large majority of the protein crystal structures strings of residues are missing. Polar residues incline to occur in missing strings together with glycine, while apolar and aromatic residues tend to avoid them. Particularly flexible residues, as shown by their extremely high B-factors, by their exposure to the solvent and by their secondary structures, flank the missing strings. These data should be a helpful guideline for crystallographers that encounter regions of flat and uninterpretable electron density as well as end-users of crystal structures.
蛋白质数据库中存入的很大一部分蛋白质晶体结构是不完整的，因为尽管某些残基是所分析材料的一部分，但一个或多个残基的位置并未报告。这可能会使分子生物学家使用蛋白质晶体结构时产生偏差。在这里我们观察到，在绝大多数蛋白质晶体结构中，残基序列是缺失的。极性残基倾向于与甘氨酸一起出现在缺失序列中，而非极性和芳香族残基则倾向于避开它们。特别灵活的残基，从其极高的B因子、暴露于溶剂的情况以及二级结构来看，位于缺失序列的两侧。这些数据对于遇到平坦且难以解释的电子密度区域的晶体学家以及晶体结构的最终用户应该是一个有用的指导。
