6I7F

Dehaloperoxidase B from Amphitrite ornata - complex with 2,4-dichlorophenol

Summary for 6I7F

• Entry DOI: 10.2210/pdb6i7f/pdb
• Descriptor: Dehaloperoxidase B, PROTOPORPHYRIN IX CONTAINING FE, 2,4-dichlorophenol, ... (5 entities in total)
• Functional Keywords: 5-bromoindole, peroxidase, globin, oxidoreductase
• Biological source: Amphitrite ornata
• Total number of polymer chains: 2
• Total formula weight: 32580.03

Authors

Moreno-Chicano, T.,Ebrahim, A.,Worrall, J.A.R.,Strange, R.W.,Axford, D.,Sherrell, D.A.,Sugimoto, H.,Tono, K.,Owada, S.,Duyvesteyn, H. (deposition date: 2018-11-16, release date: 2019-11-20, Last modification date: 2025-01-15)

Primary citation

Moreno-Chicano, T.,Ebrahim, A.,Axford, D.,Appleby, M.V.,Beale, J.H.,Chaplin, A.K.,Duyvesteyn, H.M.E.,Ghiladi, R.A.,Owada, S.,Sherrell, D.A.,Strange, R.W.,Sugimoto, H.,Tono, K.,Worrall, J.A.R.,Owen, R.L.,Hough, M.A.
High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.
Iucrj, 6:1074-1085, 2019

PubMed Abstract: High-throughput X-ray crystal structures of protein-ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein-ligand complexes using SFX.

PubMed: 31709063
DOI: 10.1107/S2052252519011655

Experimental method

X-RAY DIFFRACTION (1.85 Å)