Crystallographic Asymmetric Unit Research Articles

Structure, dimeric conformation, and coenzyme versatility of p-hydroxybenzoate hydroxylase from Arthrobacter sp. PAMC25564

p-Hydroxybenzoate hydroxylase (PHBH) catalyzes the ortho-hydroxylation of 4-hydroxybenzoate (4-HB) to protocatechuate (PCA). PHBHs are commonly known as homodimers, and the prediction of pyridine nucleotide binding and specificity remains an ongoing focus in this field. Therefore, our study aimed to determine the dimerization interface in AspPHBH from Arthrobacter sp. PAMC25564 and identify the canonical pyridine nucleotide-binding residues, along with coenzyme specificity, through site-directed mutagenesis. The results confirm a functional dimeric assembly from a tetramer that appeared in the crystallographic asymmetric unit identical to that established in previous studies. Furthermore, AspPHBH exhibits coenzyme versatility, utilizing both NADH and NADPH, with a preference for NADH. Rational engineering experiments demonstrated that targeted mutations in coenzyme surrounding residues profoundly impact NADPH binding, leading to nearly abrogated enzymatic activity compared to that of NADH. R50, R273, and S166 emerged as significant residues for NAD(P)H binding, having a near-fatal impact on NADPH binding compared to NADH. Likewise, the E44 residue plays a critical role in determining coenzyme specificity. Overall, our findings contribute to the fundamental understanding of the determinants of PHBH's active dimeric conformation, coenzyme binding and specificity holding promise for biotechnological advancements.

A survey of supramolecular association involving the oxide-O atom in the crystals of triorganoamine N-oxide derivatives, RR′R″N(+)O(−)

Abstract Trimethylamine N-oxide, Me3N(+)O(−), is an important molecule in biology and medicine. Herein, a survey of the interactions involving the oxide-O atom in crystals containing derivatives of Me3N(+)O(−), namely RR′R″N(+)O(−), is presented; R,R′, R″ = alkyl and/or aryl. A total of 119 RR′R″N(+)O(−) molecules were analysed for the supramolecular interactions involving the oxide-O atom. Hydrates form the largest class of crystals, comprising over 40 % of the 91 crystals investigated, a value slightly higher than expectation. Over 80 % of molecules had at least one O–H⋯O(−)(oxide) hydrogen bond: 3, 45 and 33 % of all molecules had three, two or one O–H⋯O(−)(oxide) hydrogen bonds, respectively. Further, nearly 15 % of molecules formed at least one N–H⋯O(−)(oxide) hydrogen bond, sometimes operating in concert with O–H⋯O(−)(oxide) hydrogen bonds. The overwhelming majority of molecules featured inter- and/or intra-molecular supporting C–H⋯O(−)(oxide) contacts so that a diverse range of supramolecular interaction patterns is apparent, a situation made more complicated by the appearance of different supramolecular association patterns often observed for independent molecules in crystals with more than one molecule in the crystallographic asymmetric-unit. Of the 6 % of molecules devoid of conventional A–H⋯O(−)(oxide) hydrogen bonds, all formed three or four inter-/intra-molecular C–H⋯O(−)(oxide) contacts usually characterised by at least one short H⋯O(−)(oxide) distance.

Variation in the zero-point energy difference via electrostatic interactions in Co(ii)-Cltpy-based spin-crossover molecular materials

The graphic illustrates the variation in the thermal spin-crossover behavior by changing their crystallographic asymmetric units. The inset depicts the ratio between the positive and negative average electrostatic interactions.

Synthesis, Crystal Structure Analyses, and Antibacterial Evaluation of the Cobalt(II) Complex with Sulfadiazine-Pyrazole Prodrug

The complex [Co(L)(H2O)4](NO3)2 of (E)-4-(2-(3-methyl-5-oxo-1-(pyridin-2-yl)-1H-pyrazol-4(5H)-ylidene)hydrazinyl)-N-(pyrimidin-2-yl)benzenesulfonamide (L) was synthesized via the self-assembly technique. Its molecular and supramolecular structures were analyzed using FTIR, elemental analyses, and single-crystal X-ray diffraction, as well as Hirshfeld calculations. This complex crystallized in the triclinic space group P1¯ with Z = 2. The crystallographic asymmetric unit comprised one complex cation and two nitrate counter anions. This complex had distorted octahedral geometry around the Co(II) ion. Numerous intermolecular interactions affecting the molecular packing of this complex were conformed using Hirshfeld investigations. The most significant contacts for the cationic inner sphere [Co(L)(H2O)4]2+ were O···H (38.8%), H···H (27.8%), and N···H (9.9%). On the other hand, the main interactions for the counter NO3¯ ions were the O···H (79.6 and 77.8%), O···N (8.0%), and O···C (9.1%). A high propensity for making interactions for each atom pair in the contacts O…H, N…C, N…H, and C…C was revealed by enrichment ratio values greater than 1. The antibacterial efficacy of the complex and the free ligand were assessed. The free ligand had higher antibacterial activity (MIC = 62.5–125 µg/mL) than the [Co(L)(H2O)4](NO3)2 complex (MIC ≥ 250 µg/mL) versus all the studied bacteria.

Crystal structures of the molecular class A β-lactamase TEM-171 and its complexes with tazobactam

The resistance of bacteria to β-lactam antibiotics is primarily caused by the production of β-lactamases. Here, novel crystal structures of the native β-lactamase TEM-171 and two complexes with the widely used inhibitor tazobactam are presented, alongside complementary data from UV spectroscopy and fluorescence quenching. The six chemically identical β-lactamase molecules in the crystallographic asymmetric unit displayed different degrees of disorder. The tazobactam intermediate was covalently bound to the catalytic Ser70 in the trans-enamine configuration. While the conformation of tazobactam in the first complex resembled that in published β-lactamase-tazobactam structures, in the second complex, which was obtained after longer soaking of the native crystals in the inhibitor solution, a new and previously unreported tazobactam conformation was observed. It is proposed that the two complexes correspond to different stages along the deacylation path of the acyl-enzyme intermediate. The results provide a novel structural basis for the rational design of new β-lactamase inhibitors.

Synthesis, crystal structure and noncovalent study of 1,5-Bis[1-(4-Fluorophenyl)ethylidene]-carbohidrazide

This work is devoted to the study of the weak interactions present in the crystal packing of a new synthesized carbohidrazide derivate. The crystal structure was determined by X-Ray single crystal diffraction. The crystallographic asymmetric unit was optimized using DFT and compared with the experimental data. The nucleophilic and electrophilic regions were carried out with the molecular electrostatic potential. Hirsfeld analysis and noncovalent interaction approach were computed to quantificate the weak interactions responsible for the arrangement and stabilization of the molecular crystal packing. These approaches provides a rich representation for the analysis of noncovalent interactions in real space, in terms of the electron density and its derivates, of Van der Waals interactions, Hydrogen Bonds and the inter and intramolecular steric repulsions. The potential biological activity as an anticancer drug was tested with the molecular docking study in the catalytic center of a human Topoisomerase.

Strategic synthon approach in obtaining cocrystals and cocrystal polymorphs of a high-Z′ system deferiprone – an anti-thalassemia drug

Compounds with more than one molecule in the crystallographic asymmetric unit (Z′ > 1) display a noticeably stronger propensity to form cocrystals. Deferiprone is an anti-thalassemia drug known to exhibit polymorphic behaviour. Previously, three polymorphs were reported out of which one of them exhibited Z′ > 1. In the present manuscript, a fourth polymorph of deferiprone was identified and it also possessed Z′ > 1. All the four polymorphs showed similar hydrogen bonding features and differed in crystal packing. The ability of deferiprone to crystallize as Z′ > 1 prompted us to investigate the hydrogen bonding and synthon variation upon cocrystallization of deferiprone with hydroxyl-group-containing coformers such as catechol, hydroquinone, phloroglucinol, resorcinol and pyrogallol. Crystallization attempts along with PXRD analysis aided in obtaining 11 new cocrystal structures which involve different stoichiometric cocrystals and some polymorphs. Synthon analysis, crystal packing as well as thermal behaviour were assessed and compared. The presence of multiple phases in each cocrystal system in its respective bulk powders was identified and quantified using PXRD and Rietveld analysis. Homosynthons were observed in three co-crystal systems, while a heterosynthon was observed in five systems. The combination of both homo- and heterosynthon was observed in three cocrystal systems. The phase transformation events were observed in most of the systems. In nine co-crystal systems, the melting points were observed intermediate between those of the API and the coformers.

Arithmetic proof of the multiplicity-weighted Euler characteristic for symmetrically arranged space-filling polyhedra.

The puzzling observation that the famous Euler's formula for three-dimensional polyhedra V - E + F = 2 or Euler characteristic χ = V - E + F - I = 1 (where V, E, F are the numbers of the bounding vertices, edges and faces, respectively, and I = 1 counts the single solid itself) when applied to space-filling solids, such as crystallographic asymmetric units or Dirichlet domains, are modified in such a way that they sum up to a value one unit smaller (i.e. to 1 or 0, respectively) is herewith given general validity. The proof provided in this paper for the modified Euler characteristic, χm = Vm - Em + Fm - Im = 0, is divided into two parts. First, it is demonstrated for translational lattices by using a simple argument based on parity groups of integer-indexed elements of the lattice. Next, Whitehead's theorem, about the invariance of the Euler characteristic, is used to extend the argument from the unit cell to its asymmetric unit components.

Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28.

Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis.

MrPIXEL: automated execution of Pixel calculations via the Mercury interface

The interpretation of crystal structures in terms of intermolecular interaction energies enables phase stability and polymorphism to be rationalized in terms of quantitative thermodynamic models, while also providing insight into the origin of physical and chemical properties including solubility, compressibility and host-guest formation. The Pixel method is a semi-empirical procedure for the calculation of intermolecular interactions and lattice energies based only on crystal structure information. Molecules are represented as blocks of undistorted ab initio molecular electron and nuclear densities subdivided into small volume elements called pixels. Electrostatic, polarization, dispersion and Pauli repulsion terms are calculated between pairs of pixels and nuclei in different molecules, with the accumulated sum equating to the intermolecular interaction energy, which is broken down into physically meaningful component terms. The MrPIXEL procedure enables Pixel calculations to be carried out with minimal user intervention from the graphical interface of Mercury, which is part of the software distributed with the Cambridge Structural Database (CSD). Following initial setup of a crystallographic model, one module assigns atom types and writes necessary input files. A second module then submits the required electron-density calculation either locally or to a remote server, downloads the results, and submits the Pixel calculation itself. Full lattice energy calculations can be performed for structures with up to two molecules in the crystallographic asymmetric unit. For more complex cases, only molecule-molecule energies are calculated. The program makes use of the CSD Python API, which is also distributed with the CSD.

Structural analysis of the putative SARS-CoV-2 primase complex

We report the crystal structure of the SARS-CoV-2 putative primase composed of the nsp7 and nsp8 proteins. We observed a dimer of dimers (2:2 nsp7-nsp8) in the crystallographic asymmetric unit. The structure revealed a fold with a helical core of the heterotetramer formed by both nsp7 and nsp8 that is flanked with two symmetry-related nsp8 β-sheet subdomains. It was also revealed that two hydrophobic interfaces one of approx. 1340 Å2 connects the nsp7 to nsp8 and a second one of approx. 950 Å2 connects the dimers and form the observed heterotetramer. Interestingly, analysis of the surface electrostatic potential revealed a putative RNA binding site that is formed only within the heterotetramer.

Unusual Magneto-Structural Features of the Halo-Substituted Materials [FeIII (5-X-salMeen)2 ]Y: a Cooperative [HS-HS]↔[HS-LS] Spin Transition.

X-ray structures of the halo-substituted complexes [FeIII (5-X-salMeen)2 ]ClO4 (X=F, Cl, Br, I) [salMeen=N-methyl-N-(2-aminoethyl)salicylaldiminate]at RT have revealed the presence of two discrete HS complex cations in the crystallographic asymmetric unit with two perchlorate counter ions linking them by N-Hamine ⋅⋅⋅Operchlorate interactions. At 90 K, the two complex cations are distinctly HS and LS, a rare crystallographic observation of this coexistence in the FeIII -salRen (R=alkyl) spin-crossover (SCO) system. At both temperatures, crystal packing shows dimerization through C-Himine ⋅⋅⋅Ophenolate interactions, a key feature for SCO cooperativity. Moreover, there are noncovalent contacts between the complex cations through type-II halogen-halogen bonds, which are novel in this system. The magnetic profiles and Mössbauer spectra concur with the structural analyses and reveal 50 % SCO of the type [HS-HS]↔[HS-LS] with a broad plateau. In contrast, [FeIII (5-Cl-salMeen)2 ]BPh4 ⋅2MeOH is LS and exhibits a temperature-dependent crystallographic phase transition, exemplifying the influence of lattice solvents and counter ions on SCO.

Crystal structure of zinc-α2-glycoprotein in complex with a fatty acid reveals multiple different modes of protein-lipid binding.

Human zinc-α2-glycoprotein (ZAG) is a 42 kDa adipokine which regulates body fat mass and is associated with cachexia and obesity. ZAG belongs to the major histocompatibility complex class I protein family and binds long-chain polyunsaturated fatty acids in its groove formed from the α1 and α2 domains. To identify the molecular basis of its lipid-binding function, we determined the first crystal structure at 2.49 Å resolution for fatty acid-bound ZAG, where the ligand was the fluorescent 11-(dansylamino)undecanoic acid (DAUDA). The 192 kDa crystallographic asymmetric unit contained six ZAG and eight fatty acid molecules in unique conformations. Six fatty acid molecules were localised to the ZAG grooves, where their tails were bound in two distinct conformations. The carboxylate groups of three fatty acids projected out of the groove, while the fourth was hydrogen bonded with R73 inside the groove. Other ligand-residue contacts were primarily hydrophobic. A new fatty acid site was revealed for two further DAUDA molecules at the ZAG α3 domains. Following conformational changes from unbound ZAG, the α3 domains formed tetrameric β-barrel structures lined by fatty acid molecules that doubled the binding capacity of ZAG. Analytical ultracentrifugation revealed that ZAG in solution was a monomer in the absence of DAUDA, but formed small amounts of tetramers with DAUDA. By showing that ZAG binds fatty acids in different locations, we demonstrate an augmented mechanism for fatty acid binding in ZAG that is distinct from other known fatty acid binding proteins, and may be relevant to cachexia.

The C-terminal region of human plasma fetuin-B is dispensable for the raised-elephant-trunk mechanism of inhibition of astacin metallopeptidases

Human fetuin-B plays a key physiological role in human fertility through its inhibitory action on ovastacin, a member of the astacin family of metallopeptidases. The inhibitor consists of tandem cystatin-like domains (CY1 and CY2), which are connected by a linker containing a “CPDCP-trunk” and followed by a C-terminal region (CTR) void of regular secondary structure. Here, we solved the crystal structure of the complex of the inhibitor with archetypal astacin from crayfish, which is a useful model of human ovastacin. Two hairpins from CY2, the linker, and the tip of the “legumain-binding loop” of CY1 inhibit crayfish astacin following the “raised-elephant-trunk mechanism” recently reported for mouse fetuin-B. This inhibition is exerted by blocking active-site cleft sub-sites upstream and downstream of the catalytic zinc ion, but not those flanking the scissile bond. However, contrary to the mouse complex, which was obtained with fetuin-B nicked at a single site but otherwise intact, most of the CTR was proteolytically removed during crystallization of the human complex. Moreover, the two complexes present in the crystallographic asymmetric unit diverged in the relative arrangement of CY1 and CY2, while the two complexes found for the mouse complex crystal structure were equivalent. Biochemical studies in vitro confirmed the differential cleavage susceptibility of human and mouse fetuin-B in front of crayfish astacin and revealed that the cleaved human inhibitor blocks crayfish astacin and human meprin α and β only slightly less potently than the intact variant. Therefore, the CTR of animal fetuin-B orthologs may have a function in maintaining a particular relative orientation of CY1 and CY2 that nonetheless is dispensable for peptidase inhibition.

The crystal structure of haemoglobin from Atlantic cod.

The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.

Synthesis and structural characterization of copper(II) complexes with a tetradentate semicarbazone ligand derived from 2,5-hexadione

Four Cu(II) complexes [CuLH2O](ClO4)2, 1; [CuLCl]Cl.H2O, 2; [CuLBr]2(Cu3Br5), 3; and [CuLH2O](NO3)2, 4; where L = tetradentate semicarbazone ligand, have been synthesized and characterized by elemental analysis, FT-IR and UV–Vis. The structures of compounds 1 and 3 have been determined by single-crystal X-ray diffraction analyses. In mononuclear 1, the semicarbazone, L acts as a tetradentate neutral ligand and a water molecule also coordinates to the Cu atom. There are two independent [CuL(H2O)]2+ cations and four perchlorate anions in the crystallographic asymmetric unit. One of the cations has a weak interaction between its Cu atom and a O atom of an adjacent perchlorate anion. The structure of 3 contains two independent [CuLBr]+ cations and a (Cu3Br5)2− anion. The coordination geometry around the cation’s Cu(II) ion is five-coordinated square pyramidal, with L acting as a tetradentate neutral ligand and with a Br at the apical position. The Cu3Br 5 2− anions link to one another to form an infinite one-dimensional (Cu3Br 5 2− )n chain. Furthermore, the Hirshfeld surface analyses and the 2D fingerprint plot have been discussed.

O-Vanillin Derived Schiff Bases and Their Organotin(IV) Compounds: Synthesis, Structural Characterisation, In-Silico Studies and Cytotoxicity.

Six new organotin(IV) compounds of Schiff bases derived from S-R-dithiocarbazate [R = benzyl (B), 2- or 4-methylbenzyl (2M and 4M, respectively)] condensed with 2-hydroxy-3-methoxybenzaldehyde (oVa) were synthesised and characterised by elemental analysis, various spectroscopic techniques including infrared, UV-vis, multinuclear (1H, 13C, 119Sn) NMR and mass spectrometry, and single crystal X-ray diffraction. The organotin(IV) compounds were synthesised from the reaction of Ph2SnCl2 or Me2SnCl2 with the Schiff bases (S2MoVaH/S4MoVaH/SBoVaH) to form a total of six new organotin(IV) compounds that had a general formula of [R2Sn(L)] (where L = Schiff base; R = Ph or Me). The molecular geometries of Me2Sn(S2MoVa), Me2Sn(S4MoVa) and Me2Sn(SBoVa) were established by X-ray crystallography and verified using density functional theory calculations. Interestingly, each experimental structure contained two independent but chemically similar molecules in the crystallographic asymmetric unit. The coordination geometry for each molecule was defined by thiolate-sulphur, phenoxide-oxygen and imine-nitrogen atoms derived from a dinegative, tridentate dithiocarbazate ligand with the remaining positions occupied by the methyl-carbon atoms of the organo groups. In each case, the resulting five-coordinate C2NOS geometry was almost exactly intermediate between ideal trigonal-bipyramidal and square-pyramidal geometries. The cytotoxic activities of the Schiff bases and organotin(IV) compounds were investigated against EJ-28 and RT-112 (bladder), HT29 (colon), U87 and SJ-G2 (glioblastoma), MCF-7 (breast) A2780 (ovarian), H460 (lung), A431 (skin), DU145 (prostate), BE2-C (neuroblastoma) and MIA (pancreatic) cancer cell lines and one normal breast cell line (MCF-10A). Diphenyltin(IV) compounds exhibited greater potency than either the Schiff bases or the respective dimethyltin(IV) compounds. Mechanistic studies on the action of these compounds against bladder cancer cells revealed that they induced the production of reactive oxygen species (ROS). The bladder cancer cells were apoptotic after 24 h post-treatment with the diphenyltin(IV) compounds. The interactions of the organotin(IV) compounds with calf thymus DNA (CT-DNA) were experimentally explored using UV-vis absorption spectroscopy. This study revealed that the organotin(IV) compounds have strong DNA binding affinity, verified via molecular docking simulations, which suggests that these organotin(IV) compounds interact with DNA via groove-binding interactions.

Near sunlight continuous broadband white-light emission by single-phase Zn(ii)-1,3,5-benzenetricarboxylate MOFs.

A new white light MOF was constructed from low-cost 1,3,5-benzenetricarboxylate and nontoxic Zinc(ii) ions. The compound possessed the most sophisticated crystallographic asymmetric unit containing sixteen metal ions and twelve ligands. Near sunlight and human eye friendly white-light emission under a wide ultraviolet radiation range of 300 to 390 nm was observed for this photoemitter, without the use of expensive rare earth and complicated organic ligands.

Evaluating the importance of fractional Z′ polymorphs in a trifluoromethylated N,N′-diphenyloxalamide derivative

A curious case of crystal dimorphism reveals an adjusted fractional number of molecules in their respective crystallographic asymmetric units.

Structural determination of archaeal UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with the bacterial cell wall intermediate UDP-N-acetylmuramic acid.

The crystal structure of UDP-N-acetylglucosamine 4-epimerase (UDP-GlcNAc 4-epimerase; WbpP; EC 5.1.3.7), from the archaeal methanogen Methanobrevibacter ruminantium strain M1, was determined to a resolution of 1.65 Å. The structure, with a single monomer in the crystallographic asymmetric unit, contained a conserved N-terminal Rossmann-fold for nucleotide binding and an active site positioned in the C-terminus. UDP-GlcNAc 4-epimerase is a member of the short-chain dehydrogenases/reductases superfamily, sharing sequence motifs and structural elements characteristic of this family of oxidoreductases and bacterial 4-epimerases. The protein was co-crystallized with coenzyme NADH and UDP-N-acetylmuramic acid, the latter an unintended inclusion and well known product of the bacterial enzyme MurB and a critical intermediate for bacterial cell wall synthesis. This is a non-native UDP sugar amongst archaea and was most likely incorporated from the E. coli expression host during purification of the recombinant enzyme.