Solution and structure of an alternating D,L-peptide
Solution and structure of an alternating D,L-peptide
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DOI：
10.1107/s0907444904022292
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发表时间：
2004-11-01
影响因子：
2.2
通讯作者：
Usón, I
中科院分区：
文献类型：
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作者：
Alexopoulos, E;Küsel, A;Usón, I
H-（L-Tyr-d-Tyr）（4）-L-Lys-OH的晶体结构已被确定为1.3埃分辨率。D，L-交替肽在四元体系中结晶，空间群P4（3）2（1）2，晶胞参数a = B = 27.99（3），c = 78.93（8）埃。晶体在不对称单元中含有两个分子，形成双链右手反平行β-螺旋。该结构已解决了SIRAS使用的晶体浸泡在含碘化物的溶液中1分钟。的程序SHELXD和SHELXE被用来确定碘化物的子结构和实验的电子密度图。利用PDB中已知的D，L-肽的坐标，进行了几次尝试，通过分子置换技术来解决结构。尽管所选MR模型的骨架显示出很大的相似性，并用于跟踪图谱中的实际肽结构，但在实验阶段可用之前，不可能获得正确的解决方案。正确的片段方向很容易确定，但这并不适用于翻译搜索。然而，从本文所述的测试中获得了对片段搜索和扩展的见解。用2.4埃左右的数据分辨率壳计算的相关系数，对应于大多数1-3个原子间矢量的距离，是在小碎片的旋转搜索中正确取向的特别好的选择。
The crystal structure of H-(L-Tyr-d-Tyr)(4)-L-Lys-OH has been determined to 1.3 Angstrom resolution. The D, L-alternating peptide crystallizes in the tetragonal system, space group P4(3)2(1)2, with unit-cell parameters a = b = 27.99 (3), c = 78.93 (8) Angstrom. The crystals contain two molecules in the asymmetric unit that form a double-stranded right-handed antiparallel beta-helix. The structure has been solved by SIRAS using a crystal soaked in an iodide-containing solution for 1 min. The programs SHELXD and SHELXE were used to determine the iodide substructure and also the experimental electron-density map. Using the coordinates of known D,L-peptides deposited in the PDB, several attempts were made to solve the structure by molecular-replacement techniques. Although the backbone of the MR model selected shows great similarity and was used to trace the actual peptide structure in the map, it was not possible to obtain the correct solution before the experimental phases became available. The correct fragment orientations are easily determined, but the same does not apply to the translation search. Nevertheless, insights into fragment search and expansion were gained from the tests described in this paper. The correlation coefficient calculated with the resolution shell of data around 2.4 Angstrom, a distance corresponding to most 1-3 interatomic vectors, is a particularly good discriminator of correct orientations in the rotation search of small fragments.