5D9C

Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data)

5D9C の概要

• エントリーDOI: 10.2210/pdb5d9c/pdb
• 関連するPDBエントリー: 5D9B 5D9D
• 分子名称: Luciferin regenerating enzyme, MAGNESIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
• 機能のキーワード: beta-prooeller, hydrolase
• 由来する生物種: Photinus pyralis (Common eastern firefly)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 34745.37

構造登録者

Yamashita, K.,Pan, D.,Okuda, T.,Murai, T.,Kodan, A.,Yamaguchi, T.,Gomi, K.,Kajiyama, N.,Kato, H.,Ago, H.,Yamamoto, M.,Nakatsu, T. (登録日: 2015-08-18, 公開日: 2015-09-23, 最終更新日: 2023-09-06)

主引用文献

Yamashita, K.,Pan, D.,Okuda, T.,Sugahara, M.,Kodan, A.,Yamaguchi, T.,Murai, T.,Gomi, K.,Kajiyama, N.,Mizohata, E.,Suzuki, M.,Nango, E.,Tono, K.,Joti, Y.,Kameshima, T.,Park, J.,Song, C.,Hatsui, T.,Yabashi, M.,Iwata, S.,Kato, H.,Ago, H.,Yamamoto, M.,Nakatsu, T.
An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5:14017-14017, 2015

PubMed Abstract: Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) holds great potential for structure determination of challenging proteins that are not amenable to producing large well diffracting crystals. Efficient de novo phasing methods are highly demanding and as such most SFX structures have been determined by molecular replacement methods. Here we employed single isomorphous replacement with anomalous scattering (SIRAS) for phasing and demonstrate successful application to SFX de novo phasing. Only about 20,000 patterns in total were needed for SIRAS phasing while single wavelength anomalous dispersion (SAD) phasing was unsuccessful with more than 80,000 patterns of derivative crystals. We employed high energy X-rays from SACLA (12.6 keV) to take advantage of the large anomalous enhancement near the LIII absorption edge of Hg, which is one of the most widely used heavy atoms for phasing in conventional protein crystallography. Hard XFEL is of benefit for de novo phasing in the use of routinely used heavy atoms and high resolution data collection.

PubMed: 26360462
DOI: 10.1038/srep14017

実験手法

X-RAY DIFFRACTION (1.6 Å)