The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: Hydration and sterochemical analysis
The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: Hydration and sterochemical analysis
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DOI：
10.1006/jmbi.2000.3597
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发表时间：
2000-03-31
影响因子：
5.6
通讯作者：
Mazzarella, L
中科院分区：
文献类型：
--
作者：
Esposito, L;Vitagliano, L;Mazzarella, L
含有67位异天冬氨酸残基的脱酰胺形式的牛胰核糖核酸酶晶体在100 K时衍射至0.87埃。我们使用所有原子的各向异性位移参数将晶体学模型改进为在61.0-0.87埃分辨率范围内所有观测反射的常规晶体学残余R = 0.101。最终模型的观测值/参数比值为7.2。这种结构是迄今为止分辨率最高的蛋白质结构之一，有趣的是，它是唯一一个在不对称单元中包含多个分子且分辨率高于1.0埃的例子。非晶体对称性已被用作几何参数的验证检查，并允许估计与此高分辨率模型相关的误差上限。在目前的结构中，有可能获得更准确的活性位点的图像，其电子密度在以前的1.9埃分辨率结构中不能清楚地解释。特别是，P1位点被硫酸盐阴离子或水分子网络交替占据。大多数氢原子在电子密度图中都是可见的，包括那些与c - α - h - α有关的氢原子……O交互。对蛋白质-溶剂相互作用的分析揭示了广泛的水分子簇的发生，主要排列在五边形融合环和周围的疏水侧链部分。最后，尽管残基样本有限，但我们已经检测到主链n - c - α - c角对残基构象的明显依赖。这种相关性可以作为蛋白质结构验证的一种有价值的工具。(C) 2000年学术出版社。
Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0.87 Angstrom at 100 K. We have refined the crystallographic model using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R = 0.101 for all observed reflections in the resolution range 61.0-0.87 Angstrom. The ratio observations /parameters is 7.2 for the final model. This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 Angstrom. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. In the present structure it was possible to obtain a more accurate picture of the active site whose electron density was not clearly interpretable in the previous 1.9 Angstrom resolution structure. In particular, the P1 site is alternatively occupied either by a sulphate anion or by a water molecule network. Most of hydrogen atoms were visible in the electron density maps, including those involved in C-alpha-H-alpha ... O interactions. Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C-alpha-C angle on residue conformation. This correlation can be fruitfully used as a valuable tool in protein structure validation. (C) 2000 Academic Press.