issue contents
August 2024 issue
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Cover illustration: Using quantum mechanics to predict histidine protonation states [Moriarty et al. (2024), Acta Cryst. D80, 639–646].
feature articles
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This article gives an overview of current trends and challenges in serial crystallography, with a focus on results from time-resolved experiments.
CCP4
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It is discussed how the metadata for the workflow from protein crystallization to the deposition of crystal structures can best be captured by using a dedicated but flexible laboratory information management system that can be either a standalone installation or a hosted service to mitigate the IT risks.
CCP-EM
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Likelihood-based cryo-EM docking using the emplace_local software is faster and more sensitive than the related em_placement software when the approximate location of a component is known. It is conveniently available through a plugin to the ChimeraX visualization software.
research papers
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The Azotobacter vinelandii FeSII protein forms an oxygen-resistant complex with the nitrogenase MoFe and Fe proteins.
PDB reference: FeSII from Azotobacter vinelandii, 6yav
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Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme have resulted in 121 binding events of 16 out of 226 investigated fragments, suggesting functional sites with respect to substrate binding and substrate channeling.
PDB references: M. tuberculosis trifunctional enzyme, complex with B-E1, 8opu; complex with B-H11, 8opv; complex with B-51, 8opw; complex with B-B3, 8opx; complex with B-77, 8opy; complex with M-1, 8oql; complex with M-10, 8oqm; complex with M-53, 8oqn; complex with M-49, 8oqo; complex with M-76, 8oqp; complex with M-79, 8oqq; complex with M-80, 8oqr; complex with M-83, 8oqs; complex with M-92, 8oqu; complex with M-109, 8oqv; complex with M-72, 8pf8
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A pragmatic method, Cryo2RT, to obtain high-throughput room-temperature structures from cryo-cooled crystals has been demonstrated and applied to ligand-binding studies.
PDB references: EP-AC39729-PF-cryo3, 7h56; EP-AC39729-PF-cryo1, 7h57; EP-AC39729-PF-RT2, 7h58; EP-AC39729-IS-cryo3, 7h59; EP-AC39729-IS-cryo1, 7h5a; EP-AC39729-IS-RT2, 7h5b; EP-AC40075-PN-cryo3, 7h5c; EP-AC40075-PN-cryo1, 7h5d; EP-AC40075-PN-RT2, 7h5e; EP-AC40075-PF-cryo3, 7h5f; EP-AC40075-PF-cryo1, 7h5g; EP-AC40075-PF-RT2, 7h5h; EP-AC40075-IS-cryo3, 7h5i; EP-AC40075-IS-cryo1, 7h5j; EP-AC40075-IS-RT2, 7h5k; EP-TL00150-PN-cryo3, 7h5l; EP-TL00150-PN-cryo1, 7h5m; EP-TL00150-PN-RT2, 7h5n; EP-TL00150-PF-cryo3, 7h5o; EP-TL00150-PF-cryo1, 7h5p; EP-TL00150-PF-RT2, 7h5q; EP-TL00150-IS-cryo3, 7h5r; EP-TL00150-IS-cryo1, 7h5s; EP-TL00150-IS-RT2, 7h5t; EP-JFD03909-PF-cryo3, 7h5u; EP-JFD03909-PF-cryo1, 7h5v; EP-JFD03909-PF-RT2, 7h5w; EP-JFD03909-IS-cryo3, 7h5x; EP-JFD03909-IS-cryo1, 7h5y; EP-JFD03909-IS-RT2, 7h5z; Thau-PF-cryo, 9fx4; Thau-PF-RT, 9fx5; 3CL-PN-cryo, 9fx6; 3CL-PN-RT, 9fx7
The first structure of a glycerol kinase from the parasite T. cruzi with a bound glycerol molecule is presented.
PDB reference: Trypanosoma cruzi glycerol kinase, 8pry
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Histidine protonation is fraught, but a new quantum-mechanical method can provide insight into choices.