Detailed assessment of X-ray induced structural perturbation in a crystalline state protein.
The positions of hydrogen atoms significantly define protein functions. However, such information from protein crystals is easily disturbed by X-rays. The damage can not be prevented completely even in the data collection at cryogenic temperatures. Therefore, the influence of X-rays should be precisely estimated in order to derive meaningful information from the crystallographic results. Diffraction data from a single crystal of the high-potential iron-sulfur protein (HiPIP) from Thermochromatium tepidum were collected at an undulator beamline of a third generation synchrotron facility, and were merged into three data sets according to X-ray dose. A series of structures analyzed at 0.70A shows detailed views of the X-ray induced perturbation, such as the positional changes of hydrogen atoms of a water molecule. Based on the results, we successfully collected a low perturbation data set using attenuated X-rays. There was no influence on the crystallographic statistics, such as the relative B factors, during the course of data collection. The electron densities for hydrogen atoms were more clear despite the slightly lower resolution.
Takeda
Kazuki
K
Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
Kusumoto
Kouji
K
Hirano
Yu
Y
Miki
Kunio
K
D001426:Bacterial Proteins / Q000737:chemistry* / Q000528:radiation effects*; D002841:Chromatiaceae / Q000737:chemistry*; D003461:Crystallography; D004307:Dose-Response Relationship, Radiation; D007506:Iron-Sulfur Proteins / Q000737:chemistry* / Q000528:radiation effects*; D008956:Models, Chemical; D008958:Models, Molecular; D045322:Photosynthetic Reaction Center Complex Proteins / Q000737:chemistry* / Q000528:radiation effects*; D011487:Protein Conformation / Q000528:radiation effects*
D001426:Bacterial Proteins; D007506:Iron-Sulfur Proteins; D045322:Photosynthetic Reaction Center Complex Proteins; C007943:high potential iron-sulfur protein