Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Acta Crystallogr D Struct Biol. 2019 Jan 1;75(Pt 1):16-20. doi: 10.1107/S205979831801519X. Epub 2019 Jan 4.
Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the FeS cubane-type cluster was created using the Cambridge Structural Database (CSD) and high-resolution structures from the Protein Data Bank. Geometries from each source were compared and pairs of refinements were performed to validate these new restraints. In addition to the restraints internal to the cluster, the CSD was mined to generate bond and angle restraints to be applied to the most common linking motif for FeS: coordination of the four Fe atoms to the side-chain sulfurs of four cysteine residues. Furthermore, computational tools were developed to assist researchers when refining FeS-containing proteins.
准确的几何约束在大分子晶体学结构精修的自动化中至关重要。使用剑桥结构数据库（CSD）和蛋白质数据库（PDB）中的高分辨率结构，为 FeS 立方烷型簇创建了一组约束。比较了每个来源的几何形状，并进行了两对精修以验证这些新约束。除了簇内的约束外，还从 CSD 中挖掘出键和角度约束，以应用于最常见的 FeS 连接基序：四个 Fe 原子与四个半胱氨酸残基侧链硫的配位。此外，还开发了计算工具来帮助研究人员在精修含 FeS 的蛋白质时使用。
