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Metal ions have important roles in supporting the catalytic activity of DNA-regulating enzymes such as topoisomerases (topos). Bacterial type II topos, gyrases and topo IV, are primary drug targets for fluoroquinolones, a class of clinically relevant antibacterials requiring metal ions for efficient drug binding. While the presence of metal ions in topos has been elucidated in biochemical studies, accurate location and assignment of metal ions in structural studies have historically posed significant challenges. Recent advances in X-ray crystallography address these limitations by extending the experimental capabilities into the long-wavelength range, exploiting the anomalous contrast from light elements of biological relevance. This breakthrough enables us to confirm experimentally the locations of Mg2+ in the fluoroquinolone-stabilized Streptococcus pneumoniae topo IV complex. Moreover, we can unambiguously identify the presence of K+ and Cl-ions in the complex with one pair of K+ ions functioning as an additional intersubunit bridge. Overall, our data extend current knowledge on the functional and structural roles of metal ions in type II topos. [ABSTRACT FROM AUTHOR]

AlphaFold2 has revolutionized structural biology by offering unparalleled accuracy in predicting protein structures. Traditional methods for determining protein structures, such as X‐ray crystallography and cryo‐electron microscopy, are often time‐consuming and resource‐intensive. AlphaFold2 provides models that are valuable for molecular replacement, aiding in model building and docking into electron density or potential maps. However, despite its capabilities, models from AlphaFold2 do not consistently match the accuracy of experimentally determined structures, need to be validated experimentally and currently miss some crucial information, such as post‐translational modifications, ligands and bound ions. In this paper, the advantages are explored of collecting X‐ray anomalous data to identify chemical elements, such as metal ions, which are key to understanding certain structures and functions of proteins. This is achieved through methods such as calculating anomalous difference Fourier maps or refining the imaginary component of the anomalous scattering factor f′′. Anomalous data can serve as a valuable complement to the information provided by AlphaFold2 models and this is particularly significant in elucidating the roles of metal ions. [ABSTRACT FROM AUTHOR]

Calcium dialuminate, CaAl4O7, nanopowders with a grossite-type structure, doped with chromium ions, were synthesized via the combined sol–gel solution combustion method. The evolution of phase composition, crystal structure, and microstructural parameters of the nanocrystalline materials depending on the temperature of the thermal treatment was investigated via X-ray powder diffraction and applying the Rietveld refinement technique. The photoluminescent properties of CaAl4O7 nanophosphors activated with Cr3+ ions were studied over the temperature range of 4.5–325 K. The samples show deep red and near-infrared luminescence due to the 2E → 4A2 and 4T2 → 4A2 energy level transitions of Cr3+ ions under excitation in the two broad emission bands in the visible spectral region. The R lines emission reveals a strong temperature dependence. The feasibility of the material for non-contact luminescence sensing is investigated, and good sensitivity is obtained based on the (R2/R1) luminescence intensity ratio and the lifetime of the emission. [ABSTRACT FROM AUTHOR]

Determination of protein crystal structures requires that the phases are derived independently of the observed measurement of diffraction intensities. Many techniques have been developed to obtain phases, including heavy-atom substitution, molecular replacement and substitution during protein expression of the amino acid methionine with selenomethionine. Although the use of selenium-containing methionine has transformed the experimental determination of phases it is not always possible, either because the variant protein cannot be produced or does not crystallize. Phasing of structures by measuring the anomalous diffraction from S atoms could in theory be almost universal since almost all proteins contain methionine or cysteine. Indeed, many structures have been solved by the so-called native sulfur single-wavelength anomalous diffraction (S-SAD) phasing method. However, the anomalous effect is weak at the wavelengths where data are normally recorded (between 1 and 2 Å) and this limits the potential of this method to well diffracting crystals. Longer wavelengths increase the strength of the anomalous signal but at the cost of increasing air absorption and scatter, which degrade the precision of the anomalous measurement, consequently hindering phase determination. A new instrument, the long-wavelength beamline I23 at Diamond Light Source, was designed to work at significantly longer wavelengths compared with standard synchrotron beamlines in order to open up the native S-SAD method to projects of increasing complexity. Here, the first novel structure, that of the oxidase domain involved in the production of the natural product patellamide, solved on this beamline is reported using data collected to a resolution of 3.15 Å at a wavelength of 3.1 Å. The oxidase is an example of a protein that does not crystallize as the selenium variant and for which no suitable homology model for molecular replacement was available. Initial attempts collecting anomalous diffraction data for native sulfur phasing on a standard macromolecular crystallography beamline using a wavelength of 1.77 Å did not yield a structure. The new beamline thus has the potential to facilitate structure determination by native S-SAD phasing for what would previously have been regarded as very challenging cases with modestly diffracting crystals and low sulfur content. [ABSTRACT FROM AUTHOR]

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required. [ABSTRACT FROM AUTHOR]

Metal ions have important roles in supporting the catalytic activity of DNA-regulating enzymes such as topoisomerases (topos). Bacterial type II topos, gyrases and topo IV, are primary drug targets for fluoroquinolones, a class of clinically relevant antibacterials requiring metal ions for efficient drug binding. While the presence of metal ions in topos has been elucidated in biochemical studies, accurate location and assignment of metal ions in structural studies have historically posed significant challenges. Recent advances in X-ray crystallography address these limitations by extending the experimental capabilities into the long-wavelength range, exploiting the anomalous contrast from light elements of biological relevance. This breakthrough enables us to confirm experimentally the locations of Mg 2+ in the fluoroquinolone-stabilized Streptococcus pneumoniae topo IV complex. Moreover, we can unambiguously identify the presence of K + and Cl - ions in the complex with one pair of K + ions functioning as an additional intersubunit bridge. Overall, our data extend current knowledge on the functional and structural roles of metal ions in type II topos., Competing Interests: Competing interests statement:The authors declare no competing interest.

In this study, we carried out a detailed investigation of the photoluminescence of Mn 4+ in Ga 2 O 3 -Al 2 O 3 solid solutions as a function of the chemical composition, temperature, and hydrostatic pressure. For this purpose, a series of (Al 1- x Ga x ) 2 O 3 :Mn 4+ ,Mg phosphors ( x = 0, ..., 0.1.0) were synthesized and characterized for the first time. A detailed crystal structure analysis of the obtained materials was done by the powder X-ray diffraction technique. The results of the crystal structure and luminescence studies evidence the transformation of the ambient-pressure-synthesized material from the rhombohedral (α-type) to monoclinic (β-type) phase as the Ga content exceeds 15%. Spectroscopic features of the Mn 4+ deep-red emission, including the temperature-dependent emission efficiency and decay time, as well as the possibility of their tuning through chemical pressure in each of these two phases were examined. Additionally, it has been shown that the application of hydrostatic pressure of ≥19 GPa allows one to obtain a corundum-like α-Ga 2 O 3 :Mn 4+ phase. The luminescence properties of this material were compared with β-Ga 2 O 3 :Mn 4+ , which is normally synthesized at ambient pressure. Finally, we evaluated the possibility of application of the studied phosphor materials for low-temperature luminescence thermometry.