Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 A resolution.
Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 A resolution.
复制标题
d(CGTAGATCTACG) 的晶体和分子结构，分辨率为 2.25 A。
DOI：
--
复制
发表时间：
1993
影响因子：
5.6
通讯作者：
W. Hunter
中科院分区：
文献类型：
--
作者：
G. Leonard;W. Hunter
用单晶X-射线衍射方法测定了合成的DNA十二聚体d（CGTAGATCTACG）的结构。该十二聚体为B-DNA的一种新晶型，属单斜晶系，空间群C2，a = 64.83 A，B = 35.36 A，c = 25.35 A，β = 92.24度。结构求解采用分子置换法，精细化采用刚体处理、分子动力学模拟退火和约束最小二乘法。在7.0至2.25 A的分辨率范围内，对于F >或= 2 sigma（F）的2120次反射，该改进的R因子为13.8%（理论上可用的78%）。不对称单元包含B型双链体（24个核苷酸，分子量7.2kDa）、136.5个水分子和50%占有率的单个镁离子。DNA模型具有标准键长0.011 A的均方根导数。该结构的中心部分是d（GATC），这是一个参与甲基化和错配修复的四联体序列。与含有这样的四分体的其他结构的比较表明在四分体水平上的多态性。在我们的结构中，观察到具有明显水合模式的狭窄小沟。这些特征在特定酶识别序列中可能是重要的。水化的一个值得注意的特征是确定了几个五角排列的氢键基团。详细的构象参数，基地堆积模式，分子间相互作用和水合作用，并与相关结构的比较。
Single crystal X-ray diffraction methods have been used to determine the structure of the synthetic DNA dodecamer d(CGTAGATCTACG). The dodecamer presents a new crystal form of B-DNA in the monoclinic system, space group C2 with a = 64.83 A, b = 35.36 A, c = 25.35 A and beta = 92.24 degrees. Structure solution was by molecular replacement and the refinement used a combination of rigid body treatment, molecular dynamics simulated annealing and restrained least-squares methods. The refinement has been concluded with an R-factor of 13.8% for 2120 reflections (78% of what is theoretically available) with F > or = 2 sigma (F) in the resolution range 7.0 to 2.25 A. The asymmetric unit comprises a B-form duplex (24 nucleotides, molecular weight 7.2 kDa), 136.5 water molecules and a single magnesium ion at 50% occupancy. The DNA model has root-mean-square derivations from standard bond lengths of 0.011 A. The central part of the structure is d(GATC), a tetrad sequence involved in methylation and mismatch repair. A comparison with other structures containing such a tetrad indicates polymorphism at the tetrad level. In our structure a narrow minor groove with a pronounced hydration pattern is observed. Such features may be of importance in the recognition of the sequence by specific enzymes. A noteworthy feature of the hydration is the identification of several pentagonal arrangements of hydrogen bonding groups. Details of conformational parameters, base stacking patterns, intermolecular interactions and hydration are presented and comparisons with related structures are given.