Swift H J, Brady L, Derewenda Z S, Dodson E J, Dodson G G, Turkenburg J P, Wilkinson A J
Department of Chemistry, University of York, Heslington, England.
Acta Crystallogr B. 1991 Aug 1;47 ( Pt 4):535-44. doi: 10.1107/s0108768191001970.
Monoclinic crystals of a neutral alpha-amylase from Aspergillus oryzae, containing three molecules in the asymmetric unit, have been reported previously and studied at 3 A resolution [Matsuura, Kunusoki, Harada & Kakudo (1984). J. Biochem. 95, 697-702]. Here we report the solution of the structure of this enzyme in a different crystal form (space group P2(1)2(1)2(1), a = 50.9, b = 67.2, c = 132.7 A), with only one molecule in the asymmetric unit. The structure was solved by the molecular replacement method, using a model of acid alpha-amylase from a related fungus A. niger [Brady, Brzozowski, Derewenda, Dodson & Dodson (1991). Acta Cryst. B47, 527-535]. Conventional least-squares crystallographic refinement failed to converge in a satisfactory manner, and the technique of molecular dynamics in the form of the XPLOR package [Brunger (1988). XPLOR Manual. Yale Univ., USA] was used to overcome the problem. A large rigid-body type movement of the C-terminal domain was identified and accounted for. The final round of restrained least-squares refinement (at 2.1 A resolution) including 3675 protein atoms and 247 water molecules resulted in a conventional crystallographic R factor of 0.183 and an atomic model which conforms well to standard stereochemical parameters (standard deviation of bond lengths from their expected values is 0.028 A, while that for planar groups is 0.029 A).
之前曾报道过米曲霉中性α-淀粉酶的单斜晶体，其不对称单元中含有三个分子，并在3 Å分辨率下进行了研究[松浦、邦之、原田及角戸（1984年）。《生物化学杂志》95卷，697 - 702页]。在此我们报道该酶在另一种晶体形式（空间群P2(1)2(1)2(1)，a = 50.9，b = 67.2，c = 132.7 Å）中的结构解析，其不对称单元中仅含一个分子。该结构通过分子置换法解析，使用了来自相关真菌黑曲霉的酸性α-淀粉酶模型[布雷迪、布罗佐夫斯基、德雷温达、多德森及多德森（1991年）。《晶体学报》B47卷，527 - 535页]。传统的最小二乘晶体学精修未能令人满意地收敛，因此使用了XPLOR软件包形式的分子动力学技术[布鲁格（1988年）。《XPLOR手册》。美国耶鲁大学]来解决该问题。确定并解释了C端结构域的一个大的刚体类型运动。最后一轮受限最小二乘精修（在2.1 Å分辨率下）包括3675个蛋白质原子和247个水分子，得到传统晶体学R因子为0.183，以及一个与标准立体化学参数非常吻合的原子模型（键长与其预期值的标准偏差为0.028 Å，平面基团的标准偏差为0.029 Å）。
