Crystallography Reports最新文献

{"title":"Protein of Unknown Function from Bacterium Variovorax paradoxus with the Amino Acid Substitution N174k Capable of Forming Schiff Base with a PLP Molecule","authors":"I. O. Ilyasov,&nbsp;M. E. Minyaev,&nbsp;T. V. Rakitina,&nbsp;A. K. Bakunova,&nbsp;V. O. Popov,&nbsp;E. Yu. Bezsudnova,&nbsp;K. M. Boyko","doi":"10.1134/S1063774524602235","DOIUrl":"10.1134/S1063774524602235","url":null,"abstract":"<p>Pyridoxal 5'-phosphate (PLP)-dependent enzymes are among the most abundant enzymes present in nearly all organisms, where they perform more than 150 different catalytic functions. Based on the three-dimensional structures, these enzymes are classified into seven (I–VII) different fold types. In these enzymes, the cofactor is bound as a Schiff base with the conserved active-site lysine residue. Recently, we have discovered the protein from the bacterium <i>Variovorax paradoxus</i> (VAPA), which belongs to the fold type IV and has a significant structural similarity to transaminases. It contains an asparagine residue at the position of catalytic lysine in fold type IV transaminases and, consequently, it cannot form a Schiff base with PLP and does not have aminotransferase activity. In this study, a single-point mutant of the VAPA protein with the N174K substitution was obtained and its three-dimensional structure was determined. An analysis of the obtained data showed that the introduced mutation restores the ability of  VAPA to form a Schiff base with the cofactor.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 6","pages":"861 - 865"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasmon Polaritons of the TE and TM Types in a Metal Film Bordering a Superlattice. I: Properties of Impedances of Semi-Infinite Media and Films","authors":"A. N. Darinskii","doi":"10.1134/S1063774524602338","DOIUrl":"10.1134/S1063774524602338","url":null,"abstract":"<p>The <i>TE-</i> and <i>TM</i>-polarized surface plasmon polaritons in a metal film placed between a periodic superlattice and a homogeneous dielectric or between two periodic superlattices have been theoretically investigated. Dispersion equations are derived in the form of the equality to zero of the determinant of a real symmetric matrix composed of the surface impedances of the media and film. Some general properties of the impedances and eigenvalues of the matrices entering the dispersion equations are established.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 6","pages":"905 - 915"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimization of the Composition of Solid Electrolytes in MF2−LaF3−NdF3 and MF2−CeF3−PrF3 (M = Ca, Sr, Ba) Systems by Room-Temperature Ionic Conductivity","authors":"N. I. Sorokin,&nbsp;D. N. Karimov","doi":"10.1134/S1063774524602144","DOIUrl":"10.1134/S1063774524602144","url":null,"abstract":"<p>In order to search for new highly conductive fluoride materials, X-ray diffraction and conductometric properties of alloys (polycrystals) of the compositions 38LaF₃^<b>.</b>57NdF₃^<b>.</b>5<i>M</i>F₂ and 47.5CeF₃^<b>.</b>47.5PrF₃^<b>.</b>5<i>M</i>F₂ (mol %) for <i>M</i> = Ca, Sr, and Ba were studied. The samples were prepared by spontaneous crystallization of homogenized melts in the <i>M</i>F₂−LaF₃−NdF₃ and <i>M</i>F₂−CeF₃−PrF₃ systems in a fluorinating atmosphere. The resulting alloys are solid solutions of the compositions (La_0.4Nd_0.6)_0.95<i>M</i>_0.05F_2.95 and (Ce_0.5Pr_0.5)_0.95<i>M</i>_0.05F_2.95 with a tysonite-type structure (sp. gr. <span>(Pbar {3}c1)</span>). The ion-conductive properties of three-component (<i>R</i>,<i>R</i>')_0.95<i>M</i>_0.05F_2.95 (<i>R</i>, <i>R</i>' = 0.4La + 0.6Nd and 0.5Ce + 0.5Pr) and two-component <i>R</i>_0.95<i>M</i>_0.95F_2.95 (<i>R</i> = La, Ce, Pr, Nd) compositions were carried out. It was found that, in the case of (Ce_0.5Pr_0.5)_0.95Sr_0.05F_2.95 polycrystals, the interior grain conductivity, equal to σ_293 K = 1.3 × 10⁻³ S/cm at room temperature, significantly exceeds the ionic conductivity of bulk Ce_0.95Sr_0.05F_2.95 and Pr_0.95Sr_0.05F_2.95 solid solution crystals, which confirms the influence of the geometric factor on the magnitude of ionic conductivity in the families of crystals with a tysonite-type structure. The study shows the prospects of further comprehensive research of three-component compositions (<i>R</i>,<i>R</i>')_0.95<i>M</i>_0.05F_2.95 to achieve the limit value of room-temperature conductivity.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 6","pages":"924 - 930"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of T5-Like Phage dUTPase from Vibrio Phage Phi3","authors":"A. S. Glukhov,&nbsp;U. F. Dzhus,&nbsp;I. A. Kolyadenko,&nbsp;G. K. Selikhanov,&nbsp;A. G. Gabdulkhakov","doi":"10.1134/S1063774524602041","DOIUrl":"10.1134/S1063774524602041","url":null,"abstract":"<p>The first crystal structure of dUTPase from the bacteriophage <i>Vibrio</i> phage phi3 was determined at 1.95 Å resolution. This protein has a homotrimeric quaternary structure characteristic of this type of dUTPases and contains a short loop in the N-terminal region of the polypeptide chain, which is specific for Т5-like bacteriophage dUTPases. It was demonstrated that, despite a low amino acid sequence homology between phage (Т5 and phi3) dUTPases, phi3 dUTPase can effectively replace phage Т5 dUTPase during the lytic cycle.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 7","pages":"1093 - 1099"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preparation and Study of the Crystal Structure of a Complex Compound Based on Cobalt, 1,5-Disulfonaphthalene, and Ethylenediamine","authors":"Zh. R. Suyunov,&nbsp;Kh. Kh. Turaev,&nbsp;Sh. A. Kasimov,&nbsp;N. A. Ermuratova,&nbsp;K. N. Kornilov","doi":"10.1134/S1063774524602053","DOIUrl":"10.1134/S1063774524602053","url":null,"abstract":"<p>A complex compound based on a divalent cobalt ion as a complexing agent and two different ligands, 1,5-disulfonaphthalene (1,5-naphthalenedisulfonic acid, Na₂NDS) and ethylenediamine, has been synthesized for the first time. The structure of the metal complex was investigated by IR and Raman spectroscopy. It was proved that the compound has a stoichiometric composition [Co(NO₃)⋅(C₂H₄(NH₂)₂)₂]<span>(_{2}^{ + })</span>⋅(C₁₀H₆O₆S₂)^2–⋅4H₂O. The complex was subjected to thermal analysis to determine its stability. Its stability, determined by the existence of intramolecular hydrogen bonds, was confirmed. Molecular rearrangements occur in the structure at 142°C, and gradual decomposition of the compound begins; in the range of 305–311°C the material studied undergoes melting, and complete destruction occurs only at 500°C. The crystal structure of the obtained metal complex was studied by X-ray diffraction analysis. A Hirshfeld surface analysis revealed intermolecular interactions between hydrogen and oxygen atoms and between hydrogen and nitrogen atoms, i.e., hydrogen bonds, stabilizing the complex.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 7","pages":"1077 - 1086"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of Different Gaseous Media in the Process of Microwave Pyrolysis Carbonization of Cellulose on the Properties of the Obtained Activated Carbon","authors":"I. G. Dyachkova,&nbsp;D. A. Zolotov,&nbsp;A. S. Kumskov,&nbsp;I. S. Volchkov,&nbsp;E. V. Matveev,&nbsp;V. V. Berestov,&nbsp;V. E. Asadchikov","doi":"10.1134/S1063774524601977","DOIUrl":"10.1134/S1063774524601977","url":null,"abstract":"<p>Comparative studies of the characteristics of high-molecular organic matter (cotton lint), subjected to pyrolytic carbonization under conditions of high-intensity microwave radiation in various gaseous media (N₂, CO₂, Ar), have been carried out. The following methods were applied: determination of the adsorption activity by methylene blue indicator, X-ray fluorescence analysis, transmission electron microscopy with microanalysis, and X-ray phase analysis. Electrodes were fabricated from carbon materials obtained by microwave carbonization using different gases, and symmetric cells were assembled according to the two-electrode scheme. Their electrochemical properties were investigated using cyclic voltammetry and galvanostatic charge–discharge methods. The materials obtained using a CO₂ gaseous medium were found to possess the best characteristics.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 6","pages":"838 - 850"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of γ Irradiation on the Optical and Energy Spectra of Fluoride Single- and Multicomponent Crystal Systems Activated by Cе3+ Ions","authors":"S. E. Sarkisov,&nbsp;V. A. Yusim,&nbsp;Yu. V. Pisarevsky","doi":"10.1134/S1063774524601862","DOIUrl":"10.1134/S1063774524601862","url":null,"abstract":"<p>The scintillation properties of LiF crystals and the family of multicomponent compounds LiF–<i>R</i>F₃ (<i>R</i> = Y, Gd), activated by Ce³⁺ ions, proposed as materials sensitive to thermal neutrons and γ radiation, are compared. An abnormally large cross section of radiative capture of thermal neutrons in gadolinium and the calculated high values of the effective charge number <i>Z</i> of multicomponent compounds determine their efficiency as neutron and gamma scintillators in comparison with LiF. The absorption spectra of unirradiated and γ-irradiated LiF crystals activated by cerium ions are analyzed. The bands of induced color centers are identified. The conversion of the ion oxidation state, Ce⁴⁺ → Ce³⁺, related to effect of γ quanta on the crystals, is investigated. The light yield of all crystals studied was determined by comparing the positions of the maxima of total absorption peaks with the position of the maximum of the total absorption peak of a standard NaI(Tl) sample in the energy spectra from a ¹³⁷Cs γ source with an energy of 662 keV. The effect of increasing the light yield under γ irradiation of LiF crystals with Ce³⁺ ions was discovered and explained in terms of the participation of γ-induced color centers (<i>F</i> and <i>F</i>^<i>-</i> centers). The possibility of increasing additionally the light efficiency due to sensitized luminescence in LiGdF₄ : Ce³⁺ crystals was analyzed.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 7","pages":"1131 - 1137"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microhardness of Metal–Polymer Composites Based on Polymer Track Membranes and FeNi Nanowires","authors":"I. M. Doludenko,&nbsp;I. S. Volchkov,&nbsp;P. L. Podkur,&nbsp;I. O. Koshelev,&nbsp;D. R. Khairetdinova,&nbsp;V. M. Kanevskii","doi":"10.1134/S1063774524601576","DOIUrl":"10.1134/S1063774524601576","url":null,"abstract":"<p>Metal–polymer composites have been obtained by matrix synthesis in pores of track membranes with different times of filling pores with permalloy. The geometric parameters of the resulting arrays of nanowires, which were the functional filling of composites, were determined using scanning electron microscopy. The microhardness of the nanocomposites was studied by the nanoindentation method. A relationship between the increase in the microhardness of the metal–polymer composite and the degree of filling the matrix is established. It is suggested that there is a relationship between the composite hardness and the number of intersections of nanowires in the matrix.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 7","pages":"1150 - 1156"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of Subunit Vaccine against African Swine Fever Virus Based on CD2v Protein Using Immunoinformatics and Molecular Dynamics Methods","authors":"A. S. Ivanovsky,&nbsp;V. I. Timofeev,&nbsp;A. V. Kalach,&nbsp;Y. V. Kordonskaya,&nbsp;M. A. Marchenkova,&nbsp;Y. V. Pisarevsky,&nbsp;Y. A. Dyakova,&nbsp;M. V. Kovalchuk","doi":"10.1134/S1063774524601953","DOIUrl":"10.1134/S1063774524601953","url":null,"abstract":"<p>A subunit vaccine against African swine fever virus (ASFV) was computationally designed using immunoinformatics and molecular dynamics methods. The three–dimensional structure of the selected immunogenic CD2v protein of ASFV was modeled and its topology relative to the membrane was predicted. The B- and T-cell epitopes for the outer-membrane part of CD2v were predicted and their immunogenicity, allergenicity, and toxicity were evaluated. For the development of a subunit vaccine, the least variable site was identified based on the analysis of the conservancy of the predicted epitopes. For the selected outer-membrane region, its stability in an aqueous salt solution was evaluated by molecular dynamics methods, which demonstrated its structural stability. The immunomodulation study showed that the developed vaccine candidate can cause a persistent immune response and does not induce a cytokine storm.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 6","pages":"877 - 885"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Three-Dimensional Reconstruction of Helical Structures from Small-Angle X-ray Scattering Data","authors":"V. A. Grigorev,&nbsp;P. V. Konarev,&nbsp;V. V. Volkov","doi":"10.1134/S106377452460203X","DOIUrl":"10.1134/S106377452460203X","url":null,"abstract":"<p>Helical particles are of interest because of their similarity to real nanostructures that are formed in processes of self-organization of biopolymers (for example, carrageenans, DNA, etc.). On the other hand, the determination of the structural parameters of such particles from small-angle X-ray scattering data is a complex issue due to the poor conditionality of the inverse problem. This is evident from the practice of using the well-known bead modeling programs. The study considers a modification of the search algorithm in a limited area of space and the behavior of the solutions depending on the parameters of the objective function responsible for the connectivity of the structure, the weight scheme for the scattering intensity curve, and the angular range of the data. The stability of the solutions was statistically assessed using a sequential model search by varying the weights of the penalty terms. The empirical dependences of the optimal values of the search parameters on the parameters of the pair distance distribution curves were determined.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":"69 6","pages":"851 - 860"},"PeriodicalIF":0.6,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}