Publisher: IUCr   (Total: 10 journals)   [Sort alphabetically]

Showing 1 - 10 of 10 Journals sorted by number of followers
Acta Crystallographica Section A: Foundations and Advances     Hybrid Journal   (Followers: 8, SJR: 5.99, CiteScore: 13)
Acta Crystallographica Section C: Structural Chemistry     Hybrid Journal   (Followers: 8, SJR: 0.834, CiteScore: 3)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 8, SJR: 0.592, CiteScore: 1)
J. of Applied Crystallography     Hybrid Journal   (Followers: 7, SJR: 1.635, CiteScore: 3)
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials     Hybrid Journal   (Followers: 6, SJR: 1.654, CiteScore: 5)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 5)
Acta Crystallographica Section E : Crystallographic Communications     Open Access   (Followers: 3, SJR: 0.153, CiteScore: 0)
J. of Synchrotron Radiation     Open Access   (Followers: 3, SJR: 1.65, CiteScore: 3)
IUCrData     Open Access   (Followers: 1)
IUCrJ     Open Access   (SJR: 3.212, CiteScore: 5)
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Acta Crystallographica Section D : Biological Crystallography
Number of Followers: 5  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1399-0047 - ISSN (Online) 2059-7983
Published by IUCr Homepage  [10 journals]
  • Crystallographic fragment-binding studies of the Mycobacterium
           tuberculosis trifunctional enzyme suggest binding pockets for the tails of
           the acyl-CoA substrates at its active sites and a potential
           substrate-channeling path between them

    • Free pre-print version: Loading...

      Authors: Dalwani; S., Metz, A., Huschmann, F.U., Weiss, M.S., Wierenga, R.K., Venkatesan, R.
      Abstract: The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α2β2 tetrameric enzyme in which the α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) active sites, and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) active site. Linear, medium-chain and long-chain 2E-enoyl-CoA molecules are the preferred substrates of MtTFE. Previous crystallographic binding and modeling studies identified binding sites for the acyl-CoA substrates at the three active sites, as well as the NAD binding pocket at the HAD active site. These studies also identified three additional CoA binding sites on the surface of MtTFE that are different from the active sites. It has been proposed that one of these additional sites could be of functional relevance for the substrate channeling (by surface crawling) of reaction intermediates between the three active sites. Here, 226 fragments were screened in a crystallographic fragment-binding study of MtTFE crystals, resulting in the structures of 16 MtTFE–fragment complexes. Analysis of the 121 fragment-binding events shows that the ECH active site is the `binding hotspot' for the tested fragments, with 41 binding events. The mode of binding of the fragments bound at the active sites provides additional insight into how the long-chain acyl moiety of the substrates can be accommodated at their proposed binding pockets. In addition, the 20 fragment-binding events between the active sites identify potential transient binding sites of reaction intermediates relevant to the possible channeling of substrates between these active sites. These results provide a basis for further studies to understand the functional relevance of the latter binding sites and to identify substrates for which channeling is crucial.
      Keywords: CoA-dependent enzymes; electrostatic surfaces; lipid metabolism; substrate channeling; tuberculosis; fatty-acid β-oxidation; Mycobacterium tuberculosis; trifunctional enzyme
      Citation: urn:issn:2059-7983
      PubDate: 2024-07-16
      DOI: 10.1107/S2059798324006557
      Issue No: Vol. 80, No. 8 (2024)
       
  • A snapshot love story: what serial crystallography has done and will do
           for us

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      Authors: Henkel; A., Oberthür, D.
      Abstract: Serial crystallography, born from groundbreaking experiments at the Linac Coherent Light Source in 2009, has evolved into a pivotal technique in structural biology. Initially pioneered at X-ray free-electron laser facilities, it has now expanded to synchrotron-radiation facilities globally, with dedicated experimental stations enhancing its accessibility. This review gives an overview of current developments in serial crystallography, emphasizing recent results in time-resolved crystallography, and discussing challenges and shortcomings.
      Keywords: serial crystallography; time-resolved; structural dynamics
      Citation: urn:issn:2059-7983
      PubDate: 2024-07-10
      DOI: 10.1107/S2059798324005588
      Issue No: Vol. 80, No. 8 (2024)
       
  • Managing macromolecular crystallographic data with a laboratory
           information management system

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      Authors: Daniel; E., Wierenga, R.K., Lehtiö, L.
      Abstract: Protein crystallography is an established method to study the atomic structures of macromolecules and their complexes. A prerequisite for successful structure determination is diffraction-quality crystals, which may require extensive optimization of both the protein and the conditions, and hence projects can stretch over an extended period, with multiple users being involved. The workflow from crystallization and crystal treatment to deposition and publication is well defined, and therefore an electronic laboratory information management system (LIMS) is well suited to management of the data. Completion of the project requires key information on all the steps being available and this information should also be made available according to the FAIR principles. As crystallized samples are typically shipped between facilities, a key feature to be captured in the LIMS is the exchange of metadata between the crystallization facility of the home laboratory and, for example, synchrotron facilities. On completion, structures are deposited in the Protein Data Bank (PDB) and the LIMS can include the PDB code in its database, completing the chain of custody from crystallization to structure deposition and publication. A LIMS designed for macromolecular crystallography, IceBear, is available as a standalone installation and as a hosted service, and the implementation of key features for the capture of metadata in IceBear is discussed as an example.
      Keywords: data management; crystallography; laboratory information management systems; LIMS; IceBear; FAIR data
      Citation: urn:issn:2059-7983
      PubDate: 2024-07-10
      DOI: 10.1107/S2059798324005680
      Issue No: Vol. 80, No. 8 (2024)
       
  • The crystal structure of Shethna protein II (FeSII) from Azotobacter
           vinelandii suggests a domain swap

    • Free pre-print version: Loading...

      Authors: Kabasakal; B.V., McFarlane, C.R., Cotton, C.A.R., Schmidt, A., Kung, A., Lieber, L., Murray, J.W.
      Abstract: The Azotobacter vinelandii FeSII protein forms an oxygen-resistant complex with the nitrogenase MoFe and Fe proteins. FeSII is an adrenodoxin-type ferredoxin that forms a dimer in solution. Previously, the crystal structure was solved [Schlesier et al. (2016), J. Am. Chem. Soc. 138, 239–247] with five copies in the asymmetric unit. One copy is a normal adrenodoxin domain that forms a dimer with its crystallographic symmetry mate. The other four copies are in an `open' conformation with a loop flipped out exposing the 2Fe–2S cluster. The open and closed conformations were interpreted as oxidized and reduced, respectively, and the large conformational change in the open configuration allowed binding to nitrogenase. Here, the structure of FeSII was independently solved in the same crystal form. The positioning of the atoms in the unit cell is similar to the earlier report. However, the interpretation of the structure is different. The `open' conformation is interpreted as the product of a crystallization-induced domain swap. The 2Fe–2S cluster is not exposed to solvent, but in the crystal its interacting helix is replaced by the same helix residues from a crystal symmetry mate. The domain swap is complicated, as it is unusual in being in the middle of the protein rather than at a terminus, and it creates arrangements of molecules that can be interpreted in multiple ways. It is also cautioned that crystal structures should be interpreted in terms of the contents of the entire crystal rather than of one asymmetric unit.
      Keywords: Shethna protein II; FeSII protein; Azotobacter vinelandii; nitrogen fixation; oxygen protection; structural biology; domain swapping
      Citation: urn:issn:2059-7983
      PubDate: 2024-07-10
      DOI: 10.1107/S2059798324005928
      Issue No: Vol. 80, No. 8 (2024)
       
 
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Publisher: IUCr   (Total: 10 journals)   [Sort alphabetically]

Showing 1 - 10 of 10 Journals sorted by number of followers
Acta Crystallographica Section A: Foundations and Advances     Hybrid Journal   (Followers: 8, SJR: 5.99, CiteScore: 13)
Acta Crystallographica Section C: Structural Chemistry     Hybrid Journal   (Followers: 8, SJR: 0.834, CiteScore: 3)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 8, SJR: 0.592, CiteScore: 1)
J. of Applied Crystallography     Hybrid Journal   (Followers: 7, SJR: 1.635, CiteScore: 3)
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials     Hybrid Journal   (Followers: 6, SJR: 1.654, CiteScore: 5)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 5)
Acta Crystallographica Section E : Crystallographic Communications     Open Access   (Followers: 3, SJR: 0.153, CiteScore: 0)
J. of Synchrotron Radiation     Open Access   (Followers: 3, SJR: 1.65, CiteScore: 3)
IUCrData     Open Access   (Followers: 1)
IUCrJ     Open Access   (SJR: 3.212, CiteScore: 5)
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