6IBN

Dye type peroxidase Aa from Streptomyces lividans: 32.8 kGy structure

Summary for 6IBN

• Entry DOI: 10.2210/pdb6ibn/pdb
• Descriptor: Deferrochelatase/peroxidase, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: dye type peroxidase, dose series, serial crystallography, heme, oxidoreductase
• Biological source: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
• Total number of polymer chains: 2
• Total formula weight: 79777.01

Authors

Ebrahim, A.,Moreno-Chicano, T.,Worrall, J.A.R.,Strange, R.W.,Axford, D.,Sherrell, D.A.,Appleby, M.,Owen, R.L. (deposition date: 2018-11-30, release date: 2019-07-31, Last modification date: 2024-01-24)

Primary citation

Ebrahim, A.,Moreno-Chicano, T.,Appleby, M.V.,Chaplin, A.K.,Beale, J.H.,Sherrell, D.A.,Duyvesteyn, H.M.E.,Owada, S.,Tono, K.,Sugimoto, H.,Strange, R.W.,Worrall, J.A.R.,Axford, D.,Owen, R.L.,Hough, M.A.
Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins.
Iucrj, 6:543-551, 2019

PubMed Abstract: An approach is demonstrated to obtain, in a sample- and time-efficient manner, multiple dose-resolved crystal structures from room-temperature protein microcrystals using identical fixed-target supports at both synchrotrons and X-ray free-electron lasers (XFELs). This approach allows direct comparison of dose-resolved serial synchrotron and damage-free XFEL serial femtosecond crystallography structures of radiation-sensitive proteins. Specifically, serial synchrotron structures of a heme peroxidase enzyme reveal that X-ray induced changes occur at far lower doses than those at which diffraction quality is compromised (the Garman limit), consistent with previous studies on the reduction of heme proteins by low X-ray doses. In these structures, a functionally relevant bond length is shown to vary rapidly as a function of absorbed dose, with all room-temperature synchrotron structures exhibiting linear deformation of the active site compared with the XFEL structure. It is demonstrated that extrapolation of dose-dependent synchrotron structures to zero dose can closely approximate the damage-free XFEL structure. This approach is widely applicable to any protein where the crystal structure is altered by the synchrotron X-ray beam and provides a solution to the urgent requirement to determine intact structures of such proteins in a high-throughput and accessible manner.

PubMed: 31316799
DOI: 10.1107/S2052252519003956

Experimental method

X-RAY DIFFRACTION (2.18 Å)