STRUCTURE OF AZURIN FROM ALCALIGENES-DENITRIFICANS REFINEMENT AT 1.8-A RESOLUTION AND COMPARISON OF THE 2 CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES
STRUCTURE OF AZURIN FROM ALCALIGENES-DENITRIFICANS REFINEMENT AT 1.8-A RESOLUTION AND COMPARISON OF THE 2 CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES
复制标题
DOI：
10.1016/0022-2836(88)90129-5
复制
发表时间：
1988-10-20
影响因子：
5.6
通讯作者：
BAKER, EN
中科院分区：
文献类型：
--
作者：
BAKER, EN
利用限制性最小二乘法对产碱杆菌中的蓝铜蛋白天青蛋白进行了晶体学结构优化。21，980个观察到的反射的最终晶体学R值为1.8埃。（1. = 0.1 nm）分辨率为0.157。晶体的不对称单元包含两个独立的天青分子，其模型包括1973个蛋白质原子，以及3个SO 42-离子和281个水分子。这两种分子的比较显示出很高的对应性。对于129个残基中的125个（仅排除链末端，残基1至2和128至129），均方根（r.m.s.）主链原子位置偏差为0.27埃。对于其他结构参数r.m.s.偏差也很低;扭转角6.58%，氢键长度0.12埃，与铜的键合为0.04埃。铜的键角为3.9 °。唯一的显著差异是在链末端和几个环中。其中一些可以归因于晶体堆积效应，其他真正的结构微观异质性。精炼已经证实铜配位最好描述为扭曲的三角平面，具有与His 46 N δ 1、His 117 N δ 1和Cys 112 S γ的强平面内键，以及与Met 121 S δ的弱得多的轴向相互作用。和Gly 45 C = O。两个N-H... S氢键表征Cys 112 S γ。作为硫醇盐（S-）硫，并可能影响可见光吸收最大值。在铜位点内和周围的原子具有非常低的迁移率，而分子中最移动的区域是链末端和二级结构元件之间的一些连接环，特别是那些在“南”端的连接环，远离铜位点。主链与侧链的氢键在“北方”端提供重要的稳定相互作用。表面特征包括His 117周围的疏水补丁，可能对电子转移很重要，His 83的SO 42-位点，以及尽管存在许多带电氨基酸残基，但一般不存在离子对。这281个水分子中有182个是以近似两倍相关的对出现的。内部没有水分子。两种天青蛋白分子共有的水位点包括表面口袋中的水位点和分子间接触区域中的水位点。它们的特点是相对较低的热参数和大量的蛋白质接触。
The structure of the blue copper protein azurin, from Alcaligenes denitrificans, has been refined crystallographically by restrained least-squares methods. The final crystallographic R value for 21,980 observed reflections to 1.8 .ANG. (1 .ANG. = 0.1 nm) resolution is 0.157. The asymmetric unit of the crystal contains two independent azurin molecules, the model for which comprises 1973 protein atoms, together with three SO42- ions, and 281 water molecules. Comparison of the two molecules shows very high correspondence. For 125 out of 129 residues (excluding only the chain termini, residues 1 to 2 and 128 to 129) the root-mean-square (r.m.s.) deviation in main-chain atom positions is 0.27 .ANG.. For other structural parameters r.m.s. deviations are also low; torsion angles 6.58%, hydrogen bond lengths 0.12 .ANG., bonds to copper 0.04 .ANG. and bond angles at the copper 3.9.degree.. The only significant differences are at the chain termini and in several loops. Some of these can be attributed to crystal packing effects, others to genuine structural microheterogeneity. Refinement has confirmed that the copper co-ordination is best described as distorted trigonal planar, with strong in-plane bonds to His46 N.delta.1, His117 N.delta.1 and Cys112 S.gamma., and much weaker axial interactions with Met121 S.delta. and Gly45 C.dbd.O. Two N-H...S hydrogen bonds characterize Cys112 S.gamma. as a thiolate (S-) sulphur and may influence the visible absorption maximum. Atoms in and around the copper site have very low mobility, whereas the most mobile regions of the molecule are the chain termini and some of the connecting loops between secondary structure elements, especially those at the "southern" end, remote from the copper site. Main-chain to side-chain hydrogen bonds supply important stabilizing interactions at the "northern" end. Surface features include the hydrophobic patch around His117, probably important for electron transfer, the SO42- site at His83, and the general absence of ion pairs, despite the presence of many charged amino acid residues. The 281 water molecules include 182 that occur as approximately twofold-related pairs. There are no internal water molecules. The water sites common to both azurin molecules include those in surface pockets and some in intermolecular contact regions. They are characterized by relatively low thermal parameters and numerous protein contacts.