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AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography Acta Cryst. D (IF 2.2) Pub Date : 2024-03-07 Justin E. Miller, Matthew P. Agdanowski, Joshua L. Dolinsky, Michael R. Sawaya, Duilio Cascio, Jose A. Rodriguez, Todd O. Yeates
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Structural determination and modeling of ciliary microtubules Acta Cryst. D (IF 2.2) Pub Date : 2024-03-07 Walton, T., Doran, M.H., Brown, A.
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Welcoming five new Co-editors Acta Cryst. D (IF 2.2) Pub Date : 2024-03-04 Charles S. Bond, Elspeth F. Garman, Randy J. Read
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Advanced exploitation of unmerged reflection data during processing and refinement with autoPROC and BUSTER Acta Cryst. D (IF 2.2) Pub Date : 2024-02-27 Vonrhein, C., Flensburg, C., Keller, P., Fogh, R., Sharff, A., Tickle, I.J., Bricogne, G.
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XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures Acta Cryst. D (IF 2.2) Pub Date : 2024-02-27 Joshua A. Hull, Cheol Lee, Jin Kyun Kim, Seon Woo Lim, Jaehyun Park, Sehan Park, Sang Jae Lee, Gisu Park, Intae Eom, Minseok Kim, HyoJung Hyun, Jacob E. Combs, Jacob T. Andring, Carrie Lomelino, Chae Un Kim, Robert McKenna
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Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii Acta Cryst. D (IF 2.2) Pub Date : 2024-02-27 Esquirol, L., Newman, J., Nebl, T., Scott, C., Vickers, C., Sainsbury, F., Peat, T.S.
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A service-based approach to cryoEM facility processing pipelines at eBIC Acta Cryst. D (IF 2.2) Pub Date : 2024-02-20 Horstmann, A., Riggs, S., Chaban, Y., Clare, D.K., de Freitas, G., Farmer, D., Howe, A., Morris, K.L., Hatton, D.
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The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria Acta Cryst. D (IF 2.2) Pub Date : 2024-02-19 Gutiérrez-Fernández, J., Hersleth, H.-P., Hammerstad, M.
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Using cryo-EM to understand the assembly pathway of respiratory complex I Acta Cryst. D (IF 2.2) Pub Date : 2024-02-19 Laube, E., Schiller, J., Zickermann, V., Vonck, J.
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Dynamics and Kinetics in Structural Biology: Unravelling Function Through Time-Resolved Structural Analysis. By Keith Moffat and Eaton E. Lattman. Wiley, New York, 2023, pp. 288. ISBN 978-1-119-69628-5. Price USD 161 (hardback), USD 128 (Kindle) Acta Cryst. D (IF 2.2) Pub Date : 2024-02-19 John R. Helliwell
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Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket Acta Cryst. D (IF 2.2) Pub Date : 2024-01-30 Huang, C.-Y., Metz, A., Lange, R., Artico, N., Potot, C., Hazemann, J., Müller, M., Dos Santos, M., Chambovey, A., Ritz, D., Eris, D., Meyer, S., Bourquin, G., Sharpe, M., Mac Sweeney, A.
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Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase Acta Cryst. D (IF 2.2) Pub Date : 2024-02-02 Marlo K. Thompson, Nidhi Sharma, Andrea Thorn, Aishwarya Prakash
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Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody Acta Cryst. D (IF 2.2) Pub Date : 2024-01-24 Papageorgiou, N., Baklouti, A., Lichière, J., Desmyter, A., Canard, B., Coutard, B., Ferron, F.
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From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons Acta Cryst. D (IF 2.2) Pub Date : 2024-01-24 Caramello, N., Royant, A.
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The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF Acta Cryst. D (IF 2.2) Pub Date : 2024-01-24 Carpentier, P., van der Linden, P., Mueller-Dieckmann, C.
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A web-based dashboard for RELION metadata visualization Acta Cryst. D (IF 2.2) Pub Date : 2024-01-24 González-Rodríguez, N., Areán-Ulloa, E., Fernández-Leiro, R.
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Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL Acta Cryst. D (IF 2.2) Pub Date : 2024-01-02 Mikhail F. Vorovitch, Valeriya R. Samygina, Evgeny Pichkur, Peter V. Konarev, Georgy Peters, Evgeny V. Khvatov, Alla L. Ivanova, Ksenia K. Tuchynskaya, Olga I. Konyushko, Anton Y. Fedotov, Grigory Armeev, Konstantin V. Shaytan, Mikhail V. Kovalchuk, Dmitry I. Osolodkin, Alexey M. Egorov, Aydar A. Ishmukhametov
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Deep residual networks for crystallography trained on synthetic data Acta Cryst. D (IF 2.2) Pub Date : 2024-01-01 Mendez, D., Holton, J.M., Lyubimov, A.Y., Hollatz, S., Mathews, I.I., Cichosz, A., Martirosyan, V., Zeng, T., Stofer, R., Liu, R., Song, J., McPhillips, S., Soltis, M., Cohen, A.E.
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Current trends in macromolecular model refinement and validation Acta Cryst. D (IF 2.2) Pub Date : 2024-01-01 Vollmar, M., Nicholls, R., Antonyuk, S.
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The TR-icOS setup at the ESRF: time-resolved microsecond UV–Vis absorption spectroscopy on protein crystals Acta Cryst. D (IF 2.2) Pub Date : 2024-01-01 Engilberge, S., Caramello, N., Bukhdruker, S., Byrdin, M., Giraud, T., Jacquet, P., Scortani, D., Biv, R., Gonzalez, H., Broquet, A., van der Linden, P., Rose, S.L., Flot, D., Balandin, T., Gordeliy, V., Lahey-Rudolph, J.M., Roessle, M., de Sanctis, D., Leonard, G.A., Mueller-Dieckmann, C., Royant, A.
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Modes and model building in SHELXE Acta Cryst. D (IF 2.2) Pub Date : 2024-01-01 Usón, I., Sheldrick, G.M.
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Using graphlet degree vectors to predict atomic displacement parameters in protein structures Acta Cryst. D (IF 2.2) Pub Date : 2023-11-21 Pražnikar, J.
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Structural mechanism of Escherichia coli cyanase Acta Cryst. D (IF 2.2) Pub Date : 2023-11-16 Jihan Kim, Youngchang Kim, Jaehyun Park, Ki Hyun Nam, Yunje Cho
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Improved joint X-ray and neutron refinement procedure in Phenix Acta Cryst. D (IF 2.2) Pub Date : 2023-11-09 Liebschner, D., Afonine, P.V., Poon, B.K., Moriarty, N.W., Adams, P.D.
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Neutron crystallographic refinement with REFMAC5 from the CCP4 suite Acta Cryst. D (IF 2.2) Pub Date : 2023-11-03 Catapano, L., Long, F., Yamashita, K., Nicholls, R.A., Steiner, R.A., Murshudov, G.N.
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The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions Acta Cryst. D (IF 2.2) Pub Date : 2023-11-03 Richardson, J.S., Williams, C.J., Chen, V.B., Prisant, M.G., Richardson, D.C.
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Anaerobic fixed-target serial crystallography using sandwiched silicon nitride membranes Acta Cryst. D (IF 2.2) Pub Date : 2023-11-01 Bjelčić, M., Sigfridsson Clauss, K.G.V., Aurelius, O., Milas, M., Nan, J., Ursby, T.
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Cocrystallization of ubiquitin–deubiquitinase complexes through disulfide linkage Acta Cryst. D (IF 2.2) Pub Date : 2023-10-25 Negron Teron, K.I., Das, C.
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Structural and functional characterization of the novel endo-α(1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae Acta Cryst. D (IF 2.2) Pub Date : 2023-10-25 Mikkelsen, M.D., Tran, V.H.N., Meier, S., Nguyen, T.T., Holck, J., Cao, H.T.T., Van, T.T.T., Thinh, P.D., Meyer, A.S., Morth, J.P.
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Domain structure and cross-linking in a giant adhesin from the Mobiluncus mulieris bacterium Acta Cryst. D (IF 2.2) Pub Date : 2023-10-20 Young, P.G., Paynter, J.M., Wardega, J.K., Middleditch, M.J., Payne, L.S., Baker, E.N., Squire, C.J.
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The impact of molecular variants, crystallization conditions and the space group on ligand–protein complexes: a case study on bacterial phosphotriesterase Acta Cryst. D (IF 2.2) Pub Date : 2023-10-20 Dym, O., Aggarwal, N., Ashani, Y., Leader, H., Albeck, S., Unger, T., Hamer-Rogotner, S., Silman, I., Tawfik, D.S., Sussman, J.L.
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Crystal structures of the DExH-box RNA helicase DHX9 Acta Cryst. D (IF 2.2) Pub Date : 2023-10-20 Lee, Y.-T., Sickmier, E.A., Grigoriu, S., Castro, J., Boriack-Sjodin, P.A.
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Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography Acta Cryst. D (IF 2.2) Pub Date : 2023-10-20 Gul, M., Yuksel, B., Bulut, H., DeMirci, H.
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Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum Acta Cryst. D (IF 2.2) Pub Date : 2023-10-20 Snajdarova, K., Marques, S.M., Damborsky, J., Bednar, D., Marek, M.
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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
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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
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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 Liu, Z., Gu, K.K., Shelby, M.L., Gilbile, D., Lyubimov, A.Y., Russi, S., Cohen, A.E., Narayanasamy, S.R., Botha, S., Kupitz, C., Sierra, R.G., Poitevin, F., Gilardi, A., Lisova, S., Coleman, M.A., Frank, M., Kuhl, T.L.
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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
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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