5TMC

Re-refinement of Thermus thermopiles DNA-directed RNA polymerase structure

5TMC の概要

• エントリーDOI: 10.2210/pdb5tmc/pdb
• 分子名称: DNA-directed RNA polymerase subunit alpha, GUANOSINE-5',3'-TETRAPHOSPHATE, DNA-directed RNA polymerase subunit beta, ... (11 entities in total)
• 機能のキーワード: symmetry downshifting, validation of symmetry, transferase
• 由来する生物種: Thermus thermophilus; 詳細
• タンパク質・核酸の鎖数: 7
• 化学式量合計: 431664.71

構造登録者

Wang, J. (登録日: 2016-10-12, 公開日: 2016-11-23, 最終更新日: 2024-11-13)

主引用文献

Wang, J.
On the validation of crystallographic symmetry and the quality of structures.
Protein Sci., 24:621-632, 2015

PubMed Abstract: In 2008, Zwart and colleagues observed that the fraction of the structures deposited in the PDB alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (NCS) was about 6%, and that this percentage was rising annually. A few years later, Poon and colleagues found that 2% of all the crystal structures in the PDB belonged to higher symmetry space groups than those assigned to them. Here, I report an analysis of the X-ray diffraction data deposited for this class of structures, which shows that most of the "pseudosymmetry" and "special NCS" that has been reported is in fact true crystallographic symmetry (CS). This distinction is important because the credibility of crystal structures depends heavily on quality control statistics such as Rfree that are unreliable when they are computed incorrectly, which they often are when CS is misidentified as "special NCS" or "pseudosymmetry". When mistakes of this kind are made, artificially low values of Rfree can give unjustified confidence in the accuracy of the reported structures.

PubMed: 25352397
DOI: 10.1002/pro.2595

実験手法

X-RAY DIFFRACTION (2.71 Å)