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Structural basis for the allosteric pathway of 4-amino-4-deoxychorismate synthase Acta Cryst. D (IF 2.2) Pub Date : 2023-09-25 Yusuke Nakamichi, Jyumpei Kobayashi, Koichi Toyoda, Masako Suda, Kazumi Hiraga, Masayuki Inui, Masahiro Watanabe
4-Amino-4-deoxychorismate synthase (ADCS), a chorismate-utilizing enzyme, is composed of two subunits: PabA and PabB. PabA is a glutamine amidotransferase that hydrolyzes glutamine into glutamate and ammonia. PabB is an aminodeoxychorismate synthase that converts chorismate to 4-amino-4-deoxychorismate (ADC) using the ammonia produced by PabA. ADCS functions under allosteric regulation between PabA
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Increasing the bulk of the 1TEL–target linker and retaining the 10×His tag in a 1TEL–CMG2-vWa construct improves crystal order and diffraction limits Acta Cryst. D (IF 2.2) Pub Date : 2023-09-25 Gajjar, P.L., Pedroza Romo, M.J., Litchfield, C.M., Callahan, M., Redd, N., Nawarathnage, S., Soleimani, S., Averett, J., Wilson, E., Lewis, A., Stewart, C., Tseng, Y.-J., Doukov, T., Lebedev, A., Moody, J.D.
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Elucidating polymorphs of crystal structures by intensity-based hierarchical clustering analysis of multiple diffraction data sets Acta Cryst. D (IF 2.2) Pub Date : 2023-09-25 Matsuura, H., Sakai, N., Toma-Fukai, S., Muraki, N., Hayama, K., Kamikubo, H., Aono, S., Kawano, Y., Yamamoto, M., Hirata, K.
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X-ray structure of the metastable SEPT14–SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization Acta Cryst. D (IF 2.2) Pub Date : 2023-09-25 Italo A. Cavini, Ashley J. Winter, Humberto D'Muniz Pereira, Derek N. Woolfson, Matthew P. Crump, Richard C. Garratt
Septins are membrane-associated, GTP-binding proteins that are present in most eukaryotes. They polymerize to play important roles as scaffolds and/or diffusion barriers as part of the cytoskeleton. α-Helical coiled-coil domains are believed to contribute to septin assembly, and those observed in both human SEPT6 and SEPT8 form antiparallel homodimers. These are not compatible with their parallel heterodimeric
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A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography Acta Cryst. D (IF 2.2) Pub Date : 2023-09-25 Zhongrui Liu, Kevin K. Gu, Megan L. Shelby, Deepshika Gilbile, Artem Y. Lyubimov, Silvia Russi, Aina E. Cohen, Sankar Raju Narayanasamy, Sabine Botha, Christopher Kupitz, Raymond G. Sierra, Fredric Poitevin, Antonio Gilardi, Stella Lisova, Matthew A. Coleman, Matthias Frank, Tonya L. Kuhl
Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection
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Crystal structures of human and mouse ketohexokinase provide a structural basis for species- and isoform-selective inhibitor design Acta Cryst. D (IF 2.2) Pub Date : 2023-09-25 Rebecca Ebenhoch, Margit Bauer, Helmut Romig, Dirk Gottschling, Jörg Thomas Kley, Niklas Heine, Alexander Weber, Ingo Uphues, Herbert Nar, Alexander Pautsch
A molecular understanding of the proteins involved in fructose metabolism is essential for controlling the current spread of fructose-related obesity, diabetes and related adverse metabolic states in Western populations. Fructose catabolism starts with the phosphorylation of d-fructose to fructose 1-phosphate by ketohexokinase (KHK). KHK exists in two alternatively spliced isoforms: the hepatic and
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Michael James (1940–2023) Acta Cryst. D (IF 2.2) Pub Date : 2023-09-15 Glover, J.N.M., Kay, C.M., Lemieux, J., Read, R.J.
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Predicted models and CCP4 Acta Cryst. D (IF 2.2) Pub Date : 2023-08-17 Simpkin, A.J., Caballero, I., McNicholas, S., Stevenson, K., Jiménez, E., Sánchez Rodríguez, F., Fando, M., Uski, V., Ballard, C., Chojnowski, G., Lebedev, A., Krissinel, E., Usón, I., Rigden, D.J., Keegan, R.M.
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Correcting systematic errors in diffraction data with modern scaling algorithms Acta Cryst. D (IF 2.2) Pub Date : 2023-08-16 Aldama, L.A., Dalton, K.M., Hekstra, D.R.
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A Python package based on robust statistical analysis for serial crystallography data processing Acta Cryst. D (IF 2.2) Pub Date : 2023-08-16 Hadian-Jazi, M., Sadri, A.
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Raimond B. G. Ravelli (25 March 1968–30 June 2023) Acta Cryst. D (IF 2.2) Pub Date : 2023-08-14 Elspeth F. Garman
Raimond B. G. Ravelli is remembered.
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Novel starting points for fragment-based drug design against mycobacterial thioredoxin reductase identified using crystallographic fragment screening Acta Cryst. D (IF 2.2) Pub Date : 2023-08-14 Füsser, F.T., Wollenhaupt, J., Weiss, M.S., Kümmel, D., Koch, O.
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LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments Acta Cryst. D (IF 2.2) Pub Date : 2023-08-10 Pletzer-Zelgert, J., Ehrt, C., Fender, I., Griewel, A., Flachsenberg, F., Klebe, G., Rarey, M.
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Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership Acta Cryst. D (IF 2.2) Pub Date : 2023-08-10 Xu, W., Velankar, S., Patwardhan, A., Hoch, J.C., Burley, S.K., Kurisu, G.
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Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin Acta Cryst. D (IF 2.2) Pub Date : 2023-08-10 Tripathi, P., Mousa, J.J., Guntaka, N.S., Bruner, S.D.
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Rhizobium etli has two l-asparaginases with low sequence identity but similar structure and catalytic center Acta Cryst. D (IF 2.2) Pub Date : 2023-07-26 Joanna I. Loch, Paulina Worsztynowicz, Joanna Sliwiak, Marta Grzechowiak, Barbara Imiolczyk, Kinga Pokrywka, Mateusz Chwastyk, Miroslaw Gilski, Mariusz Jaskolski
The genome of Rhizobium etli, a nitrogen-fixing bacterial symbiont of legume plants, encodes two l-asparaginases, ReAIV and ReAV, that have no similarity to the well characterized enzymes of class 1 (bacterial type) and class 2 (plant type). It has been hypothesized that ReAIV and ReAV might belong to the same structural class 3 despite their low level of sequence identity. When the crystal structure
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A standard descriptor for fixed-target serial crystallography Acta Cryst. D (IF 2.2) Pub Date : 2023-07-18 Owen, R.L., de Sanctis, D., Pearson, A.R., Beale, J.H.
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Structural and biochemical insights into purine-based drug molecules in hBRD2 delineate a unique binding mode opening new vistas in the design of inhibitors of the BET family Acta Cryst. D (IF 2.2) Pub Date : 2023-07-11 Aishwarya H. Arole, Prashant Deshmukh, Ashok Sridhar, Shruti Mathur, Mahesh Mahalingaswamy, Hosahalli Subramanya, Nandakumar Dalavaikodihalli Nanjaiah, Balasundaram Padmanabhan
The bromodomain and extra-terminal (BET) family proteins, which are involved in chromatin function, have been shown to be promising drug targets in several pathological conditions, including cancer and inflammation. There is considerable interest in the development of BET inhibitors with novel scaffolds to modulate the epigenesis of such diseases. Here, high-resolution crystal structures of the purine
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Overall protein structure quality assessment using hydrogen-bonding parameters Acta Cryst. D (IF 2.2) Pub Date : 2023-07-11 Afonine, P.V., Sobolev, O.V., Moriarty, N.W., Terwilliger, T.C., Adams, P.D.
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The structure of the RBD–E77 Fab complex reveals neutralization and immune escape of SARS-CoV-2 Acta Cryst. D (IF 2.2) Pub Date : 2023-07-11 Zhichao Zhang, Xiaoxiong Li, Ying Xue, Bo Yang, Yuanyuan Jia, Shichao Liu, Defen Lu
The spike protein (S) of SARS-CoV-2 is the major target of neutralizing antibodies and vaccines. Antibodies that target the receptor-binding domain (RBD) of S have high potency in preventing viral infection. The ongoing evolution of SARS-CoV-2, especially mutations occurring in the RBD of new variants, has severely challenged the development of neutralizing antibodies and vaccines. Here, a murine monoclonal
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3D structures of the Plasmodium vivax subtilisin-like drug target SUB1 reveal conformational changes to accommodate a substrate-derived α-ketoamide inhibitor Acta Cryst. D (IF 2.2) Pub Date : 2023-07-11 Mariano Martinez, Fernando A. Batista, Manon Maurel, Anthony Bouillon, Laura Ortega Varga, Anne Marie Wehenkel, Lucile Le Chevalier-Sontag, Arnaud Blondel, Ahmed Haouz, Jean-François Hernandez, Pedro M. Alzari, Jean-Christophe Barale
The constant selection and propagation of multi-resistant Plasmodium sp. parasites require the identification of new antimalarial candidates involved in as-yet untargeted metabolic pathways. Subtilisin-like protease 1 (SUB1) belongs to a new generation of drug targets because it plays a crucial role during egress of the parasite from infected host cells at different stages of its life cycle. SUB1 is
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Raynals, an online tool for the analysis of dynamic light scattering Acta Cryst. D (IF 2.2) Pub Date : 2023-07-10 Burastero, O., Draper-Barr, G., Raynal, B., Chevreuil, M., England, P., Garcia Alai, M.
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Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases Acta Cryst. D (IF 2.2) Pub Date : 2023-07-10 Moroz, O.V., Blagova, E., Lebedev, A.A., Skov, L.K., Pache, R.A., Schnorr, K.M., Kiemer, L., Friis, E.P., Nymand-Grarup, S., Ming, L., Ye, L., Klausen, M., Cohn, M.T., Schmidt, E.G.W., Davies, G.J., Wilson, K.S.
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Crystal structure of dihydrofolate reductase from the emerging pathogenic fungus Candida auris Acta Cryst. D (IF 2.2) Pub Date : 2023-07-10 Kirkman, T., Sketcher, A., de Morais Barroso, V., Ishida, K., Tosin, M., Dias, M.V.B
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Thermostable homologues of the periplasmic siderophore-binding protein CeuE from Geobacillus stearothermophilus and Parageobacillus thermoglucosidasius Acta Cryst. D (IF 2.2) Pub Date : 2023-07-10 Blagova, E.V., Miller, A.H., Bennett, M., Booth, R.L., Dodson, E.J., Duhme-Klair, A.-K., Wilson, K.S.
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AlphaFold and the future of structural biology Acta Cryst. D (IF 2.2) Pub Date : 2023-06-28 Randy J. Read, Edward N. Baker, Charles S. Bond, Elspeth F. Garman, Mark J. van Raaij
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Bulk-solvent and overall scaling revisited: faster calculations, improved results. Corrigendum. Acta Cryst. D (IF 2.2) Pub Date : 2023-06-20 Afonine, P.V., Grosse-Kunstleve, R.W., Adams, P.D., Urzhumtsev, A.
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Conformation-based refinement of 18-mer DNA structures Acta Cryst. D (IF 2.2) Pub Date : 2023-06-20 Svoboda, J., Berdár, D., Kolenko, P., Černý, J., Nováková, Z., Pavlíček, J., Schneider, B.
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Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp. Acta Cryst. D (IF 2.2) Pub Date : 2023-06-16 Eppinger, E., Stolz, A., Ferraroni, M.
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Structure–function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role Acta Cryst. D (IF 2.2) Pub Date : 2023-06-16 Kosinas, C., Zerva, A., Topakas, E., Dimarogona, M.
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Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM Acta Cryst. D (IF 2.2) Pub Date : 2023-06-16 Herreros, D., Krieger, J.M., Fonseca, Y., Conesa, P., Harastani, M., Vuillemot, R., Hamitouche, I., Serrano Gutiérrez, R., Gragera, M., Melero, R., Jonic, S., Carazo, J.M., Sorzano, C.O.S.
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Sequence-assignment validation in protein crystal structure models with checkMySequence Acta Cryst. D (IF 2.2) Pub Date : 2023-06-14 Chojnowski, G.
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Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data Acta Cryst. D (IF 2.2) Pub Date : 2023-06-14 Yu-Meng Jiang, Han Miao, Xin-Yu Pan, Qi Wang, Zheng Dong, Zhi Geng, Yu-Hui Dong
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Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis Acta Cryst. D (IF 2.2) Pub Date : 2023-06-14 Hang Wang, Xiaomei Sun, Wataru Saburi, Saki Hashiguchi, Jian Yu, Toyoyuki Ose, Haruhide Mori, Min Yao
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Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF Acta Cryst. D (IF 2.2) Pub Date : 2023-06-14 Gäfe, S., Niemann, H.H.
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Protein–macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin–sulfonato-calix[8]arene complex Acta Cryst. D (IF 2.2) Pub Date : 2023-06-14 Mockler, N.M., Ramberg, K.O., Crowley, P.B.
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Unravelling the secrets of multi-domain lytic polysaccharide monooxygenases (LPMOs) Acta Cryst. D (IF 2.2) Pub Date : 2023-05-30 Vaaje-Kolstad, G., Eijsink, V.G.H.
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Continuous development in macromolecular crystallography with CCP4 Acta Cryst. D (IF 2.2) Pub Date : 2023-05-30 Martinez-Ripoll, M., Albert, A.
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The CCP4 suite: integrative software for macromolecular crystallography Acta Cryst. D (IF 2.2) Pub Date : 2023-05-30 Agirre, J., Atanasova, M., Bagdonas, H., Ballard, C.B., Baslé, A., Beilsten-Edmands, J., Borges, R.J., Brown, D.G., Burgos-Mármol, J.J., Berrisford, J.M., Bond, P.S., Caballero, I., Catapano, L., Chojnowski, G., Cook, A.G., Cowtan, K.D., Croll, T.I., Debreczeni, J.É., Devenish, N.E., Dodson, E.J., Drevon, T.R., Emsley, P., Evans, G., Evans, P.R., Fando, M., Foadi, J., Fuentes-Montero, L., Garman, E
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Structural and binding studies of a new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii Acta Cryst. D (IF 2.2) Pub Date : 2023-06-01 Yong Zhou, Suttipong Wannapaiboon, Methinee Prongjit, Soraya Pornsuwan, Jeerus Sucharitakul, Nuntaporn Kamonsutthipaijit, Robert C. Robinson, Wipa Suginta
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Structural and functional investigation of a fungal member of carbohydrate esterase family 15 with potential specificity for rare xylans Acta Cryst. D (IF 2.2) Pub Date : 2023-05-25 Mazurkewich, S., Scholzen, K.C., Brusch, R.H., Poulsen, J.-C.N., Theibich, Y., Hüttner, S., Olsson, L., Larsbrink, J., Lo Leggio, L.
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Near-atomic resolution reconstructions from in situ revitrified cryo samples Acta Cryst. D (IF 2.2) Pub Date : 2023-05-23 Bongiovanni, G., Harder, O.F., Voss, J.M., Drabbels, M., Lorenz, U.J.
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Analysis and validation of overall N-glycan conformation in Privateer Acta Cryst. D (IF 2.2) Pub Date : 2023-05-23 Dialpuri, J.S., Bagdonas, H., Atanasova, M., Schofield, L.C., Hekkelman, M.L., Joosten, R.P., Agirre, J.
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Structure-based discovery of an antipsychotic drug, paliperidone, as a modulator of human superoxide dismutase 1: a potential therapeutic target in amyotrophic lateral sclerosis Acta Cryst. D (IF 2.2) Pub Date : 2023-05-19 Snehal Aouti, Sivaraman Padavattan, Balasundaram Padmanabhan
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Cysteine synthase: multiple structures of a key enzyme in cysteine synthesis and a potential drug target for Chagas disease and leishmaniasis Acta Cryst. D (IF 2.2) Pub Date : 2023-05-19 Sowerby, K., Freitag-Pohl, S., Murillo, A.M., Silber, A.M., Pohl, E.
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The type III secretion chaperone SctY may shield the hydrophobic export gate-binding C-terminus of its substrate SctX Acta Cryst. D (IF 2.2) Pub Date : 2023-05-19 Gilzer, D., Kowal, J.L., Flottmann, F., Niemann, H.H.
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Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain Acta Cryst. D (IF 2.2) Pub Date : 2023-05-19 Mhaindarkar, V.P., Rasche, R., Kümmel, D., Rudolph, M.G., Klostermeier, D.
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GEMMI and Servalcat restrain REFMAC5 Acta Cryst. D (IF 2.2) Pub Date : 2023-05-05 Yamashita, K., Wojdyr, M., Long, F., Nicholls, R.A., Murshudov, G.N.
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Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone Acta Cryst. D (IF 2.2) Pub Date : 2023-04-26 Miyagi, H., Suzuki, M., Yasunaga, M., Asada, H., Iwata, S., Saito, J.
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SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology Acta Cryst. D (IF 2.2) Pub Date : 2023-04-24 Alan Hicks, Paul Abraham, Wellington Leite, Qiu Zhang, Kevin L. Weiss, Hugh O'Neill, Loukas Petridis, Jeremy C. Smith
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Conformational transition of the Ixodes ricinus salivary serpin Iripin-4 Acta Cryst. D (IF 2.2) Pub Date : 2023-04-24 Kascakova, B., Kotal, J., Havlickova, P., Vopatkova, V., Prudnikova, T., Grinkevich, P., Kuty, M., Chmelar, J., Kuta Smatanova, I.
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Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases Acta Cryst. D (IF 2.2) Pub Date : 2023-04-18 Zhen-Lang Xie, Chang Yuan, Zhao-Hui Zhou
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FLEXR: automated multi-conformer model building using electron-density map sampling Acta Cryst. D (IF 2.2) Pub Date : 2023-04-18 Stachowski, T.R., Fischer, M.
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Structural and functional characterization of a multi-domain GH92 α-1,2-mannosidase from Neobacillus novalis Acta Cryst. D (IF 2.2) Pub Date : 2023-04-18 Kołaczkowski, B.M., Moroz, O.V., Blagova, E., Davies, G.J., Møller, M.S., Meyer, A.S., Westh, P., Jensen, K., Wilson, K.S., Krogh, K.B.R.M.
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The T2 structure of polycrystalline cubic human insulin Acta Cryst. D (IF 2.2) Pub Date : 2023-04-11 Triandafillidis, D.P., Karavassili, F., Spiliopoulou, M., Valmas, A., Athanasiadou, M., Nikolaras, G., Fili, S., Kontou, P., Bowler, M.W., Chasapis, C.T., Von Dreele, R.B., Fitch, A.N., Margiolaki, I.
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Introduction to the virtual thematic issue on room-temperature biological crystallography Acta Cryst. D (IF 2.2) Pub Date : 2023-04-04 Roberto A. Steiner
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Conformation-dependent ligand hot spots in the spliceosomal RNA helicase BRR2 Acta Cryst. D (IF 2.2) Pub Date : 2023-04-28 Vester, K., Metz, A., Huber, S., Loll, B., Wahl, M.C.
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The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report. Corrigendum Acta Cryst. D (IF 2.2) Pub Date : 2023-03-30 Irène Barbarin-Bocahu, Marc Graille
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The structure of the complex between the arsenite oxidase from Pseudorhizobium banfieldiae sp. strain NT-26 and its native electron acceptor cytochrome c552 Acta Cryst. D (IF 2.2) Pub Date : 2023-03-30 Poddar, N., Santini, J.M., Maher, M.J.