5GX2

Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 3.4 MGy (3rd measurement)

Summary for 5GX2

• Entry DOI: 10.2210/pdb5gx2/pdb
• Related: 5GX1 5GX3 5GX4 5GX5
• Descriptor: Luciferin regenerating enzyme, MERCURY (II) ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: beta-prooeller, hydrolase
• Biological source: Photinus pyralis (Common eastern firefly)
• Total number of polymer chains: 1
• Total formula weight: 34955.63

Authors

Hasegawa, K.,Yamashita, K.,Murai, T.,Nuemket, N.,Hirata, K.,Ueno, G.,Ago, H.,Nakatsu, T.,Kumasaka, T.,Yamamoto, M. (deposition date: 2016-09-15, release date: 2017-01-04, Last modification date: 2023-11-08)

Primary citation

Hasegawa, K.,Yamashita, K.,Murai, T.,Nuemket, N.,Hirata, K.,Ueno, G.,Ago, H.,Nakatsu, T.,Kumasaka, T.,Yamamoto, M.
Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24:29-41, 2017

PubMed Abstract: Serial crystallography, in which single-shot diffraction images are collected, has great potential for protein microcrystallography. Although serial femtosecond crystallography (SFX) has been successfully demonstrated, limited beam time prevents its routine use. Inspired by SFX, serial synchrotron crystallography (SSX) has been investigated at synchrotron macromolecular crystallography beamlines. Unlike SFX, the longer exposure time of milliseconds to seconds commonly used in SSX causes radiation damage. However, in SSX, crystals can be rotated during the exposure, which can achieve efficient coverage of the reciprocal space. In this study, mercury single-wavelength anomalous diffraction (Hg-SAD) phasing of the luciferin regenerating enzyme (LRE) was performed using serial synchrotron rotation crystallography. The advantages of rotation and influence of dose on the data collected were evaluated. The results showed that sample rotation was effective for accurate data collection, and the optimum helical rotation step depended on multiple factors such as multiplicity and partiality of reflections, exposure time per rotation angle and the contribution from background scattering. For the LRE microcrystals, 0.25° was the best rotation step for the achievable resolution limit, whereas a rotation step larger than or equal to 1° was favorable for Hg-SAD phasing. Although an accumulated dose beyond 1.1 MGy caused specific damage at the Hg site, increases in resolution and anomalous signal were observed up to 3.4 MGy because of a higher signal-to-noise ratio.

PubMed: 28009544
DOI: 10.1107/S1600577516016362

Experimental method

X-RAY DIFFRACTION (1.6 Å)