5WR2

Thermolysin, SFX liganded form with oil-based carrier

Summary for 5WR2

• Entry DOI: 10.2210/pdb5wr2/pdb
• Related: 5WR3 5WR4 5WR5 5WR6
• Descriptor: Thermolysin, N-[(benzyloxy)carbonyl]-L-aspartic acid, ZINC ION, ... (5 entities in total)
• Functional Keywords: x-ray free-electron laser, serial femtosecond crystallography, microcrystal, structure-based drug design, hydrolase
• Biological source: Geobacillus stearothermophilus
• Cellular location: Secreted : P43133
• Total number of polymer chains: 1
• Total formula weight: 34853.29

Authors

Kunishima, N.,Naitow, H.,Matsuura, Y. (deposition date: 2016-11-29, release date: 2017-08-16, Last modification date: 2023-11-08)

Primary citation

Naitow, H.,Matsuura, Y.,Tono, K.,Joti, Y.,Kameshima, T.,Hatsui, T.,Yabashi, M.,Tanaka, R.,Tanaka, T.,Sugahara, M.,Kobayashi, J.,Nango, E.,Iwata, S.,Kunishima, N.
Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation
Acta Crystallogr D Struct Biol, 73:702-709, 2017

PubMed Abstract: Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.

PubMed: 28777085
DOI: 10.1107/S2059798317008919

Experimental method

X-RAY DIFFRACTION (2 Å)