McCoy, Airlie J Stockwell, Duncan H Sammito, Massimo D Oeffner, Robert D Hatti, Kaushik S Croll, Tristan I Read, Randy J
Published in
Acta crystallographica. Section D, Structural biology
Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a small chance of being correct. Accelerating this move has been improvements in phasing methods, which are now able to extract ...
Cragnolini, Tristan Sahota, Harpal Joseph, Agnel Praveen Sweeney, Aaron Malhotra, Sony Vasishtan, Daven Topf, Maya
Published in
Acta crystallographica. Section D, Structural biology
Structural determination of molecular complexes by cryo-EM requires large, often complex processing of the image data that are initially obtained. Here, TEMPy2, an update of the TEMPy package to process, optimize and assess cryo-EM maps and the structures fitted to them, is described. New optimization routines, comprehensive automated checks and wo...
Sehnal, David Svobodová, Radka Berka, Karel Rose, Alexander S Burley, Stephen K Velankar, Sameer Koča, Jaroslav
Published in
Acta crystallographica. Section D, Structural biology
Biomacromolecular structural data make up a vital and crucial scientific resource that has grown not only in terms of its amount but also in its size and complexity. Furthermore, these data are accompanied by large and increasing amounts of experimental data. Additionally, the macromolecular data are enriched with value-added annotations describing...
Nakamura, Hirohiko Takahashi, Sachiko Inaka, Koji Tanaka, Hiroaki
Published in
Acta crystallographica. Section D, Structural biology
A large high-quality crystal is required to specify the positions of H atoms in neutron structural analysis. Consequently, several methods have been proposed for obtaining such large crystals, and theoretical considerations for growing them have been presented. However, further investigation is required to obtain a numerical model that can provide ...
de Paiva, Fernanda C R Chan, Karen Samborskyy, Markiyan Silber, Ariel M Leadlay, Peter F Dias, Marcio V B
Published in
Acta crystallographica. Section D, Structural biology
Adenylate-forming enzymes (AFEs) are a mechanistic superfamily of proteins that are involved in many cellular roles. In the biosynthesis of benzoxazole antibiotics, an AFE has been reported to play a key role in the condensation of cyclic molecules. In the biosynthetic gene cluster for the benzoxazole AJI9561, AjiA1 catalyzes the condensation of tw...
Kolenko, Petr Svoboda, Jakub Černý, Jiří Charnavets, Tatsiana Schneider, Bohdan
Published in
Acta crystallographica. Section D, Structural biology
Solution and crystal data are reported for DNA 18-mers with sequences related to those of bacterial noncoding single-stranded DNA segments called repetitive extragenic palindromes (REPs). Solution CD and melting data showed that the CG-rich, near-palindromic REPs from various bacterial species exhibit dynamic temperature-dependent and concentration...
Khramtsov, Yuri V Vlasova, Anastasiia D Vlasov, Alexey V Rosenkranz, Andrey A Ulasov, Alexey V Ryzhykau, Yury L Kuklin, Alexander I Orekhov, Anton S Eydlin, Ilia B Georgiev, Georgii P
...
Published in
Acta crystallographica. Section D, Structural biology
Modular nanotransporters (MNTs) are multifunctional chimeric polypeptides for the multistep transport of locally acting cytotoxic agents into the nuclei of cancer target cells. MNTs consist of several polypeptide domains (functional modules) for the recognition of a cell-surface internalizable receptor, pH-dependent endosomal escape and subsequent ...
Moriarty, Nigel W Liebschner, Dorothee Tronrud, Dale E Adams, Paul D
Published in
Acta crystallographica. Section D, Structural biology
Crystallographic refinement of macromolecular structures relies on stereochemical restraints to mitigate the typically poor data-to-parameter ratio. For proteins, each amino acid has a unique set of geometry restraints which represent stereochemical information such as bond lengths, valence angles, torsion angles, dihedrals and planes. It has been ...
Wang, Lum Kruse, Holger Sobolev, Oleg V Moriarty, Nigel W Waller, Mark P Afonine, Pavel V Biczysko, Malgorzata
Published in
Acta crystallographica. Section D, Structural biology
Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is...
Sridhar, Shruthi Schmitz, Werner Hiltunen, J Kalervo Venkatesan, Rajaram Bergmann, Ulrich Kiema, Tiila Riikka Wierenga, Rikkert K
Published in
Acta crystallographica. Section D, Structural biology
The peroxisomal multifunctional enzyme type 1 (MFE1) catalyzes two successive reactions in the β-oxidation cycle: the 2E-enoyl-CoA hydratase (ECH) and NAD+-dependent 3S-hydroxyacyl-CoA dehydrogenase (HAD) reactions. MFE1 is a monomeric enzyme that has five domains. The N-terminal part (domains A and B) adopts the crotonase fold and the C-terminal p...
