IUCrJ最新文献

{"title":"Quantum refinement in real and reciprocal space using the Phenix and ORCA software","authors":"","doi":"10.1107/S2052252524008406","DOIUrl":"10.1107/S2052252524008406","url":null,"abstract":"<div><div>We present a new implementation of quantum refinement interfacing the widely used <em>Phenix</em> and <em>ORCA</em> software. We show applications on a neutron structure of Mn superoxide dismutase, X-ray structures of V- and Fe-nitrogenase and a cryo-EM structure of particulate methane monooxygenase.</div></div><div><div>X-ray and neutron crystallography, as well as cryogenic electron microscopy (cryo-EM), are the most common methods to obtain atomic structures of biological macromolecules. A feature they all have in common is that, at typical resolutions, the experimental data need to be supplemented by empirical restraints, ensuring that the final structure is chemically reasonable. The restraints are accurate for amino acids and nucleic acids, but often less accurate for substrates, inhibitors, small-molecule ligands and metal sites, for which experimental data are scarce or empirical potentials are harder to formulate. This can be solved using quantum mechanical calculations for a small but interesting part of the structure. Such an approach, called quantum refinement, has been shown to improve structures locally, allow the determination of the protonation and oxidation states of ligands and metals, and discriminate between different interpretations of the structure. Here, we present a new implementation of quantum refinement interfacing the widely used structure-refinement software <em>Phenix</em> and the freely available quantum mechanical software <em>ORCA</em>. Through application to manganese superoxide dismutase and V- and Fe-nitro­genase, we show that the approach works effectively for X-ray and neutron crystal structures, that old results can be reproduced and structural discrimination can be performed. We discuss how the weight factor between the experimental data and the empirical restraints should be selected and how quantum mechanical quality measures such as strain energies should be calculated. We also present an application of quantum refinement to cryo-EM data for particulate methane monooxygenase and show that this may be the method of choice for metal sites in such structures because no accurate empirical restraints are currently available for metals.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using deep-learning predictions reveals a large number of register errors in PDB depositions","authors":"","doi":"10.1107/S2052252524009114","DOIUrl":"10.1107/S2052252524009114","url":null,"abstract":"<div><div>A novel structure-validation method is applied to PDB depositions at 3–5 Å resolution, revealing large numbers of putative register errors.</div></div><div><div>The accuracy of the information in the Protein Data Bank (PDB) is of great importance for the myriad downstream applications that make use of protein structural information. Despite best efforts, the occasional introduction of errors is inevitable, especially where the experimental data are of limited resolution. A novel protein structure validation approach based on spotting inconsistencies between the residue contacts and distances observed in a structural model and those computationally predicted by methods such as <em>AlphaFold</em>2 has previously been established. It is particularly well suited to the detection of register errors. Importantly, this new approach is orthogonal to traditional methods based on stereochemistry or map–model agreement, and is resolution independent. Here, thousands of likely register errors are identified by scanning 3–5 Å resolution structures in the PDB. Unlike most methods, the application of this approach yields suggested corrections to the register of affected regions, which it is shown, even by limited implementation, lead to improved refinement statistics in the vast majority of cases. A few limitations and confounding factors such as fold-switching proteins are characterized, but this approach is expected to have broad application in spotting potential issues in current accessions and, through its implementation and distribution in <em>CCP</em>4, helping to ensure the accuracy of future depositions.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142465949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tuning structural modulation and magnetic properties in metal–organic coordination polymers [CH3NH3]CoxNi1−x(HCOO)3","authors":"","doi":"10.1107/S2052252524008583","DOIUrl":"10.1107/S2052252524008583","url":null,"abstract":"<div><div>We show that the modulated phase transitions in solid solutions of [CH₃NH₃]Co_<em>x</em>Ni_{1−<em>x</em>}(HCOO)₃, with <em>x</em> = 0.25 (<strong>1</strong>), <em>x</em> = 0.50 (<strong>2</strong>) and <em>x</em> = 0.75 (<strong>3</strong>), can be tuned by the metal ratio, which offers the opportunity to consciously build molecular compounds with adjustable properties by doping metal sites.</div></div><div><div>Three solid solutions of [CH₃NH₃]Co<em>_x</em>Ni_{1−<em>x</em>}(HCOO)₃, with <em>x</em> = 0.25 (<strong>1</strong>), <em>x</em> = 0.50 (<strong>2</strong>) and <em>x</em> = 0.75 (<strong>3</strong>), were synthesized and their nuclear structures and magnetic properties were characterized using single-crystal neutron diffraction and magnetization measurements. At room temperature, all three compounds crystallize in the <em>Pnma</em> orthorhombic space group, akin to the cobalt and nickel end series members. On cooling, each compound undergoes a distinct series of structural transitions to modulated structures. Compound <strong>1</strong> exhibits a phase transition to a modulated structure analogous to the pure Ni compound [Cañadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodríguez-Carvajal, J. &amp; Petricek, V. (2020). <em>Inorg. Chem.</em><strong>59</strong>, 17896–17905], whereas compound <strong>3</strong> maintains the behaviour observed in the pure Co compound reported previously [Canadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodriguez-Velamazan, J. A. &amp; Rodriguez-Carvajal, J. (2019). <em>IUCrJ</em>, <strong>6</strong>, 105–115], although in both cases the temperatures at which the phase transitions occur differ slightly from the pure phases. Monochromatic neutron diffraction measurements showed that the structural evolution of <strong>2</strong> diverges from that of either parent compound, with competing hydrogen bond interactions that drive the modulation throughout the series, producing a unique sequence of phases. It involves two modulated phases below 96 (3) and 59 (3) K, with different <strong>q</strong> vectors, similar to the pure Co compound (with modulated phases below 128 and 96 K); however, it maintains the modulated phase below magnetic order [at 22.5 (7) K], resembling the pure Ni compound (which presents magnetic order below 34 K), resulting in an improper modulated magnetic structure. Despite these large-scale structural changes, magnetometry data reveal that the bulk magnetic properties of these solid solutions form a linear continuum between the end members. Notably, doping of the metal site in these solid solutions allows for tuning of bulk magnetic properties, including magnetic ordering temperature, transition temperatures and the nature of nuclear phase transitions, through adjustment of metal ratios.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis, structural and spectroscopic characterization of defect-rich forsterite as a representative phase of Martian regolith","authors":"","doi":"10.1107/S2052252524009722","DOIUrl":"10.1107/S2052252524009722","url":null,"abstract":"<div><div>Ball milling of forsterite (Mg₂SiO₄) was carried out to mimic mechanical weathering processes on Mars. The defective forsterite structure models, capable of describing both long-range and short-range order, are deduced by density functional theory assisted pair distribution function analysis.</div></div><div><div>Regolith draws intensive research attention because of its importance as the basis for fabricating materials for future human space exploration. Martian regolith is predicted to consist of defect-rich crystal structures due to long-term space weathering. The present report focuses on the structural differences between defect-rich and defect-poor forsterite (Mg₂SiO₄) – one of the major phases in Martian regolith. In this work, forsterites were synthesized using reverse strike co-precipitation and high-energy ball milling (BM). Subsequent post-processing was also carried out using BM to enhance the defects. The crystal structures of the samples were characterized by X-ray powder diffraction and total scattering using Cu and synchrotron radiation followed by Rietveld refinement and pair distribution function (PDF) analysis, respectively. The structural models were deduced by density functional theory assisted PDF refinements, describing both long-range and short-range order caused by defects. The Raman spectral features of the synthetic forsterites complement the <em>ab initio</em> simulation for an in-depth understanding of the associated structural defects.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography","authors":"","doi":"10.1107/S2052252524010170","DOIUrl":"10.1107/S2052252524010170","url":null,"abstract":"<div><div>Structures of the dark-adapted state of a photoactivated adenylate cyclase were determined from serial crystallography (SX) data collected at room temperature at an X-ray free-electron laser and a synchrotron, and are compared with cryo-macromolecular crystallography (MX) synchrotron structures obtained by us and others. These structures of the wild-type enzyme in combination with the cryo-MX synchrotron structure of a light-sensor domain mutant provide insight into the hydrogen-bond network rearrangement upon blue-light illumination and pave the way for the determination of structural intermediates of the enzyme by time-resolved SX.</div></div><div><div>OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium <em>Oscillatoria acuminata</em> that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied pico­second–millisecond spectroscopic intermediates.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unity gives strength: combining Bertaut’s and Belov’s concepts and the formalism of aperiodic crystals to solve magnetic structures of unprecedented complexity","authors":"","doi":"10.1107/S2052252524010182","DOIUrl":"10.1107/S2052252524010182","url":null,"abstract":"<div><div>We draw attention to the exceptional work of Geers <em>et al.</em>[(2024). <em>IUCrJ</em>, <strong>11</strong>, 910–920] on the analysis of magnetic phases, in which challenging magnetic structures are determined by a combination of modern computational methods and a connection between nuclear modulation and the ordering of magnetic moments is shown.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of MltG from Mycobacterium abscessus reveals structural plasticity between composed domains","authors":"","doi":"10.1107/S2052252524008443","DOIUrl":"10.1107/S2052252524008443","url":null,"abstract":"<div><div>We provide the structure of MltG of the lytic transglycosyl­ase family in this study. We show that MltG has a flexible peptidoglycan-binding domain and exists as a monomer in solution. Further, the putative active site of <em>Mycobacterium abscessus</em> MltG has been revealed using structural analysis and sequence comparison. This research significantly advances our comprehension of the transglycosyl­ation process mediated by the MltG family, providing valuable insights that can inform the development of next-generation antibiotics to specifically target <em>M. abscessus</em>.</div></div><div><div>MltG, a membrane-bound lytic transglycosyl­ase, has roles in terminating glycan polymerization in peptidoglycan and incorporating glycan chains into the cell wall, making it significant in bacterial cell-wall biosynthesis and remodeling. This study provides the first reported MltG structure from <em>Mycobacterium abscessus</em> (maMltG), a superbug that has high antibiotic resistance. Our structural and biochemical analyses revealed that MltG has a flexible peptidoglycan-binding domain and exists as a monomer in solution. Further, the putative active site of maMltG was disclosed using structural analysis and sequence comparison. Overall, this study contributes to our understanding of the transglycosyl­ation reaction of the MltG family, aiding the design of next-generation antibiotics targeting <em>M. abscessus.</em></div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Waterless structures in the Protein Data Bank","authors":"","doi":"10.1107/S2052252524009928","DOIUrl":"10.1107/S2052252524009928","url":null,"abstract":"<div><div>A global analysis of protein crystal structures in the Protein Data Bank reveals many medium-to-high-resolution entries that lack any solvent molecules. Also, there are many cases with impossible occupancies of water molecules and/or uninterpreted very high difference electron-density peaks that indicate the presence of unmodeled water molecules.</div></div><div><div>The absence of solvent molecules in high-resolution protein crystal structure models deposited in the Protein Data Bank (PDB) contradicts the fact that, for proteins crystallized from aqueous media, water molecules are always expected to bind to the protein surface, as well as to some sites in the protein interior. An analysis of the contents of the PDB indicated that the expected ratio of the number of water molecules to the number of amino-acid residues exceeds 1.5 in atomic resolution structures, decreasing to 0.25 at around 2.5 Å resolution. Nevertheless, almost 800 protein crystal structures determined at a resolution of 2.5 Å or higher are found in the current release of the PDB without any water molecules, whereas some other depositions have unusually low or high occupancies of modeled solvent. Detailed analysis of these depositions revealed that the lack of solvent molecules might be an indication of problems with either the diffraction data, the refinement protocol, the deposition process or a combination of these factors. It is postulated that problems with solvent structure should be flagged by the PDB and addressed by the depositors.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Roodmus: a toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions","authors":"","doi":"10.1107/S2052252524009321","DOIUrl":"10.1107/S2052252524009321","url":null,"abstract":"<div><div><em>Roodmus</em> is a toolkit sourcing conformational heterogeneity of biomacromolecules from molecular dynamics simulations to generate high-quality synthetic data for the development and benchmarking of heterogeneous reconstruction algorithms.</div></div><div><div>Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be reconstructed. However, the conformation space accessible to these molecules is continuous and, therefore, explored incompletely by a small number of discrete classes. Recently developed heterogeneous reconstruction algorithms (HRAs) to analyse continuous heterogeneity rely on machine-learning methods that employ low-dimensional latent space representations. The non-linear nature of many of these methods poses a challenge to their validation and interpretation and to identifying functionally relevant conformational trajectories. These methods would benefit from in-depth benchmarking using high-quality synthetic data and concomitant ground truth information. We present a framework for the simulation and subsequent analysis with respect to the ground truth of cryo-EM micrographs containing particles whose conformational heterogeneity is sourced from molecular dynamics simulations. These synthetic data can be processed as if they were experimental data, allowing aspects of standard SPA workflows as well as heterogeneous reconstruction methods to be compared with known ground truth using available utilities. The simulation and analysis of several such datasets are demonstrated and an initial investigation into HRAs is presented.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142465948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry","authors":"","doi":"10.1107/S2052252524005785","DOIUrl":"10.1107/S2052252524005785","url":null,"abstract":"<div><p>The determination of a challenging structure in the <em>P</em>1 space group, the lowest symmetry possible, shows how our <em>in situ</em> serial crystallography approach expands the application of crystallization plates as a robust sample delivery method.</p></div><div><p>The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (<em>e.g.</em> large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct <em>in situ</em> data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an <em>in situ</em> serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry <em>P</em>1 space group at 3.0 Å resolution. Our <em>in situ</em> data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141616469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}