2BLR

Thaumatin Before A High Dose X-Ray "Burn"

2BLR の概要

• エントリーDOI: 10.2210/pdb2blr/pdb
• 関連するPDBエントリー: 1KWN 1LR2 1LR3 1LXZ 1LY0 1PP3 1RQW 1THI 1THU 1THV 1THW 2BLR
• 分子名称: THAUMATIN I, L(+)-TARTARIC ACID (3 entities in total)
• 機能のキーワード: radiation damage, synchrotron, phasing, rip, plant protein, taste-modifying protein
• 由来する生物種: THAUMATOCOCCUS DANIELLII (MIRACLE FRUIT, KATEMFE)
• 細胞内の位置: Cytoplasmic vesicle: P02883
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 22306.07

構造登録者

Nanao, M.H.,Ravelli, R. (登録日: 2005-03-08, 公開日: 2005-09-07, 最終更新日: 2024-11-13)

主引用文献

Nanao, M.H.,Sheldrick, G.M.,Ravelli, R.B.
Improving Radiation-Damage Substructures for Rip.
Acta Crystallogr.,Sect.D, 61:1227-, 2005

PubMed Abstract: Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.

PubMed: 16131756
DOI: 10.1107/S0907444905019360

実験手法

X-RAY DIFFRACTION (1.4 Å)