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Gluconate 5-dehydrogenase (Ga5DH; EC 1.1.1.69) from Lentibacter algarum (LaGa5DH) was recombinantly expressed in Escherichia coli and purified to homogeneity. The protein was crystallized and the crystal structure was solved at 2.1 Å resolution. The crystal belonged to the monoclinic system, with space group P1 and unit-cell parameters a = 55.42, b = 55.48, c = 79.16 Å, α = 100.51, β = 105.66, γ = 97.99°. The structure revealed LaGaDH to be a tetramer, with each subunit consisting of six α-helices and three antiparallel β-hairpins. LaGa5DH has high structural similarity to other Ga5DH proteins, demonstrating that this enzyme is highly conserved.

The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic and eukaryotic cells. Three proteins, PA5086, PA5087 and PA5088, are employed to suppress the toxicity of PldB-family proteins. The structures of PA5087 and PA5088 have previously been reported, but the identification of further distinctions between these immunity proteins is needed. Here, the crystal structure of PA5086 is reported at 1.90 Å resolution. A structural comparison of the three PldB immunity proteins showed vast divergences in their electrostatic potential surfaces. This interesting phenomenon provides an explanation of the stockpiling mechanism of T6SS immunity proteins.

The transmembrane intracellular lectin ER–Golgi intermediate compartment protein 53 (ERGIC-53) and the soluble EF-hand multiple coagulation factor deficiency protein 2 (MCFD2) form a complex that functions as a cargo receptor, trafficking various glycoproteins between the endoplasmic reticulum (ER) and the Golgi apparatus. It has been demonstrated that the carbohydrate-recognition domain (CRD) of ERGIC-53 (ERGIC-53CRD) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53CRD complexed with MCFD2 and mannosyl oligosaccharides have revealed protein–protein and protein–sugar binding modes. In contrast, the polypeptide-recognition mechanism of MCFD2 remains largely unknown. Here, a 1.60 Å resolution crystal structure of the ERGIC-53CRD–MCFD2 complex is reported, along with three other crystal forms. Comparison of these structures with those previously reported reveal that MCFD2, but not ERGIC-53–CRD, exhibits significant conformational plasticity that may be relevant to its accommodation of various polypeptide ligands.

The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and l-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.

Solution structure of β-amylase 2 from Arabidopsis thaliana shows the role of the conserved N-terminus in enzyme tetramer formation.

A new scaling program is presented with new features to support multi-sweep workflows and analysis within the DIALS software package.

This article presents an overview of the development of two basic software libraries for image manipulation and data visualization in cryo-EM: emcore and emvis.

From the perspective of a young(ish) structural biologist who currently specialises in macromolecular X-ray crystallography, are the best years of crystallography over? Some evidence and hopefully thought-provoking analysis is presented here on the subject.

The paper reports the structure of a Δ1-pyrroline-2-carboxylate reductase from the archaeon Thermococcus litoralis, a key enzyme involved in the second step of trans-4-Hydroxy-L-proline metabolism, conserved in archaea, bacteria and humans.

The asymmetric unit of the title MOF, [Zn5(C14H5NO10S2)2(OH)2(H2O)10]n comprises three ZnII atoms, one of which is located on a centre of inversion, a tetra-negative carboxyl­ate ligand, one μ3-hydroxide and five water mol­ecules, each of which is coordinated. The ZnII atom, lying on a centre of inversion, is coordinated by trans sulfoxide-O atoms and four water mol­ecules in an octa­hedral geometry. Another ZnII atom is coordinated by two carboxyl­ate-O atoms, one hy­droxy-O, one sulfoxide-O and a water-O atom to define a distorted trigonal–bipyramidal geometry; a close Zn⋯O(carboxyl­ate) inter­action derived from an asymmetrically coordinating ligand (Zn—O = 1.95 and 3.07 Å) suggests a 5 + 1 coordination geometry. The third ZnII atom is coordinated in an octa­hedral fashion by two hy­droxy-O atoms, one carboxyl­ate-O, one sulfoxide-O and two water-O atoms, the latter being mutually cis. In all, the carboxyl­ate ligand binds six ZnII ions leading to a three-dimensional architecture. In the crystal, all acidic donors form hydrogen bonds to oxygen acceptors to contribute to the stability of the three-dimensional architecture.

In the title 1:1 co-crystal [systematic name: 6-chloro­pyridin-2-amine–penta­nedioic acid (1/1)], C5H5ClN2·C5H8O4, the pyridine ring is essentially planar, with a maximum deviation of 0.003 (1) Å. The base and acid mol­ecules are linked via N—H⋯O and O—H⋯N hydrogen bonds, while inversion-related acid mol­ecules are linked via pairs of O—H⋯O hydrogen bonds. These inter­actions together with a C—H⋯O hydrogen bond connect the two components, forming (001) sheets.

The title compound, [Co(NCS)2(C15H22N2O2)2] or C32H44CoN6O4S2, was prepared from cobalt(II) nitrate, benzyl carbazate and ammonium thio­cyanate in the presence of 4-hepta­none. The compound crystallizes with two centrosymmetric complexes in which the cobalt(II) atoms have a trans-CoO2N4 octa­hedral coordination geometry. In the crystal, N—H⋯S, C—H⋯S and C—H⋯.π contacts stack the complex mol­ecules along the b-axis direction.

In the title compound, [Ba(C10H20O5)2][Zn(NCS)4], the 15-crown-5 mol­ecules are disordered over two positions with site occupancies of 0.706 (4) and 0.294 (4). The Ba2+ ions are sandwiched between the 15-crown-5 rings and Zn2+ ions are surrounded by four N atoms from the thio­cyanate ligands in a distorted tetra­hedral geometry. The crystal studied was refined as an inversion twin.

In the title compound, [Cd2(C9H6O5)2(H2O)2]n, the crystallographically distinct CdII cations are coordinated in penta­gonal–bipyramidal and octa­hedral fashions. The 2-(carb­oxy­meth­oxy)benzoate (cmb) ligands connect the Cd atoms into [Cd2(cmb)2(H2O)2)]n coordination polymer ribbons that are oriented along the a-axis direction. Supra­molecular layers are formed parallel to (01overline{1}) by O—H⋯O hydrogen bonding between the ribbons. The supra­molecular three-dimensional crystal structure of the title compound is then constructed by π–π stacking inter­actions with a centroid–centroid distance of 3.622 (2) Å between cmb ligands in adjacent layer motifs.

In the title compound, C14H14ClFN2O2S, the di­hydro­pyrimidine ring adopts a shallow-boat conformation and subtends a dihedral angle of 81.91 (17)° with the phenyl ring. In the crystal, N—H⋯O, N—H⋯S and C—H⋯F hydrogen bonds and C—H⋯π inter­actions are found.

In the title compound, C11H10N2OS, the dihedral angle between the thio­phene and pyridine rings is 77.79 (8)°. In the crystal, inversion dimers linked by pairs of N—H⋯N hydrogen bonds generate R22(10) loops. The dimers are reinforced by pairs of C—H⋯N inter­actions and C—H⋯O inter­actions link the dimers into [010] chains.

In the title compound, [Cd(C10H8O4)(H2O)2)]n, the CdII cation is coordinated in a distorted trigonal–prismatic fashion. 3-(4-Carb­oxy­phen­yl)propionate (cpp) ligands connect the CdII cations into zigzag [Cd(cpp)(H2O)2)]n coordination polymer chains, which are oriented parallel to [101]. The chains aggregate into supra­molecular layers oriented parallel to (10overline{1}) by means of O—H⋯O hydrogen bonding between bound water mol­ecules and ligating cpp carboxyl­ate O atoms. The layers stack in an ABAB pattern along [100] via other O—H⋯O hydrogen-bonding mechanisms also involving the bound water mol­ecules. The crystal studied was an inversion twin.

In the title compound, [Zn(C9H6O4)]n, the ZnII cations are coordinated in a tetra­hedral fashion by carboxyl­ate O-atom donors belonging to four 4-(carb­oxy­meth­yl) benzoate (4-cmb) ligands. Each 4-cmb ligand binds to four ZnII cations in an exo­tetra­dentate fashion to create a non-inter­penetrated [Zn(4-cmb)]n three-dimensional coordination polymer network with a new non-diamondoid 66 topology. The crystal studied was refined as an inversion twin.

In the title complex, [Ni(C7H3NO4)(C15H11N3)]·C3H7NO·H2O, the NiII ion is six-coordinated within an octa­hedral geometry defined by three N atoms of the 2,2':6',2''-terpyridine ligand, and two O atoms and the N atom of the pyridine-2,6-di­carboxyl­ate di-anion. In the crystal, the complex mol­ecules are stacked in columns parallel to the a axis being connected by π–π stacking [closest inter-centroid separation between pyridyl rings = 3.669 (3) Å]. The connections between columns and solvent mol­ecules to sustain a three-dimensional architecture are of the type water-O—H⋯O(carbon­yl) and pyridyl-, methyl-C—H⋯O(carbon­yl).

The title tetra­nuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex mol­ecules, A and B, in the asymmetric unit together with 1.5 mol­ecules of chloro­form. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex mol­ecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex mol­ecules are linked by a number of C—H⋯O hydrogen bonds within the layers and between the layers, forming a supra­molecular three-dimensional structure.

The title compound, d-(+)-glucosa­mmonium potassium tetra­thio­cyanato­cobaltate(II) dihydrate, K(C6H14NO5)[Co(NCS)4]·2H2O or (GlcNH)(K)[Co(NCS)4]·2H2O, has been obtained as a side product of an incomplete salt metathesis reaction of d-(+)-glucosa­mine hydro­chloride (GlcN·HCl) and K2[Co(NCS)4]. The asymmetric unit contains a d-(+)-glucos­ammonium cation, a potassium cation, a tetra­iso­thio­cyanato­cobalt(II) complex anion and two water mol­ecules. The water mol­ecules coordinate to the potassium cation, which is further coordinated via three short K+⋯SCN− contacts involving three [Co(NCS)4]2− complex anions and via three O atoms of two d-(+)-glucosa­mmonium cations, leading to an overall eightfold coordination around the potassium cation. Hydrogen-bonding inter­actions between the building blocks consolidate the three-dimensional arrangement.

The asymmetric unit of the title compound, C8H15N3S, contains two independent mol­ecules. In both mol­ecules, the seven-membered cyclo­heptane ring adopts a chair conformation. An intra­molecular N—H⋯N hydrogen bond is observed in both mol­ecules, forming S(5) graph-set motifs. In the crystal, the two independent mol­ecules are connected through N—H⋯S hydrogen bonds, forming dimers which are in turn further connected by N—H⋯S hydrogen bonds into chains along [010].

The title compound, C6H3BrN2, also known as 3-bromo­picolino­nitrile, was synthesized by cyanation of 2,3-di­bromo­pyridine. In the solid state, short inter­molecular Br⋯N contacts are observed. Additionally, the crystal packing is consolidated by π–π stacking inter­actions with centroid–centroid distances of 3.7893 (9) Å.

The title complex, [Os3(C2H4N)H(CO)10] or [Os3(CO)10(μ-H)(μ-HN=C—CH3-1κN:2κC)], was synthesized in 41.6% yield by reactions between Os3(CO)11(CH3CN) and 2,4,6-tri­methyl­hexa­hydro-1,3,5-triazine. The central osmium triangle has two OsI atoms bridged by a hydride ligand and a μ-HN= C—CH3-1κN:2κC triazine fragment. Three CO ligands complete the coordination sphere around each OsI atom, while the remaining Os0 atom has four CO ligands. Each Os atom exhibits a pseudo-octa­hedral coordination environment, discounting the bridging Os—Os bond.

The title compound (systematic name: bis­{[2-(4-hy­droxy-1H-indol-3-yl)eth­yl]bis­(propan-2-yl)aza­nium} but-2-enedioate tetra­hydrate), 2C16H25N2O+·C4H2O42−·4H2O, has a singly protonated DPT cation, one half of a fumarate dianion (completed by a crystallographic centre of symmetry) and two water mol­ecules of crystallization in the asymmetric unit. A series of N—H⋯O and O—H⋯O hydrogen bonds form a three-dimensional network in the solid state.

The title compound, C26H22O2P+·PF6−·C4H7O, crystallizes as a cation-anion pair with a single solvent mol­ecule in the asymmetric unit. Hydrogen bonding occurs between the carb­oxy­lic acid group on the cation and the oxygen atom of the solvent mol­ecule. Longer hydrogen-bonding inter­actions are observed between fluorine atoms of the anion and H atoms on the phenyl rings of the cation.

The title compound, C12H11N3O2S, was synthesized by a condensation reaction of 2-acetyl­indan-1,3-dione and thio­semicarbazide in ethanol in the presence of glacial acetic acid. The mol­ecule adopts a thio­ketone form. The dihedral angle between the mean planes of 1H-inden-1,3(2H)-dione and hydrazinecarbo­thio­amide units is 86.32 (7)°. Weak intra­molecular N—H⋯O and C—H⋯O hydrogen bonds are observed. In the crystal, mol­ecules are linked via pairs of weak inter­molecular N—H⋯O hydrogen bonds, forming inversion dimers. The dimers are further linked into a three-dimensional network through N—H⋯S and N—H⋯O hydrogen bonds, and π–π inter­actions [centroid–centroid distances = 3.5619 (10)–3.9712 (9) Å].

The title compound, C22H22O5, crystallizes with two mol­ecules in the asymmetric unit, one of which shows disorder of its ethyl acetate group over two sets of sites in a 0.880 (2):0.120 (2) ratio. The C≡C distances in the two mol­ecules are almost the same [1.1939 (16) and 1.199 (2) Å], but the Csp3—C≡C angles differ somewhat [175.92 (12) and 172.53 (16)°]. In the crystal, several weak C—H⋯O inter­actions are seen.

In the title compound, [Pd(C7H3NO4)(C10H8N2)]·H2O, the PdII cation is four-coordinated in a distorted square-planar coordination geometry defined by the two N atoms of the 2,2'-bi­pyridine ligand, one O atom and one N atom from the pyridine-2,6-di­carboxyl­ate anion. The complex and solvent water mol­ecule are linked by inter­molecular hydrogen bonds. In the crystal, the complex mol­ecules are stacked in columns along the a axis.

In the title compound, C29H26ClNO4, the di­hydro­pyridine ring adopts a shallow boat conformation. The mean plane of the di­hydro­pyridine ring (all atoms) subtends dihedral angles of 66.54 (1), 73.71 (1) and 79.47 (1)° with the two phenyl rings and the chloro­phenyl ring, respectively. In the crystal, N—H⋯O hydrogen bonds link the mol­ecules into [001] chains.

In the title compound, C18H16N2O2, the dihedral angle between the pyrrole rings is 79.47 (9)°, with the N—H groups approximately orthogonal (H—N⋯N—H pseudo torsion angle = −106°). In the crystal, N—H⋯O hydrogen bonds link the mol­ecules into [11overline{1}] chains. A C—H⋯O inter­action is also observed.

In the title hydrated Schiff base, C13H12N4O3·H2O, the dihedral angle between the aromatic rings is 5.06 (11)° and an intra­molecular O—H⋯N hydrogen bond closes an S(6) ring. In the crystal, Ow—H⋯O and Ow—H⋯N (w = water) hydrogen bonds link the components into centrosymmetric tetra­mers (two Schiff bases and two water mol­ecules). Longer N—H⋯O hydrogen bonds link the tetra­mers into [010] chains. A weak C—H⋯O hydrogen bond and aromatic π–π stacking between the pyrazine and phenyl rings [centroid–centroid separations = 3.604 (2) and 3.715 (2) Å] are also observed.

In the title compound, C16H21N3O4, the 1,4-di­hydro­pyridine ring adopts a flattened boat conformation, with the imidazole substituent in an axial orientation [dihedral angle between ring planes = 82.9 (6)°]. In the crystal structure, pairs of N—H⋯O and N—H⋯N hydrogen bonds with graph-set notation R22(14) connect the mol­ecules into chains running along the c-axis direction.

The title carbonate hydrate, Cs2Mg4(CO3)5·10H2O, was crystallized at room temperature out of aqueous solutions containing caesium bicarbonate and magnesium nitrate. Its monoclinic crystal structure (P21/n) consists of double chains of composition 1∞[Mg(H2O)2/1(CO3)3/3], isolated [Mg(H2O)(CO3)2]2– units, two crystallographically distinct Cs+ ions and a free water mol­ecule. The crystal under investigation was twinned by reticular pseudomerohedry.

In the title compound, C10H13N5, the piperidine ring adopts a chair conformation with the exocyclic N—C bond in an axial orientation, and the dihedral angle between the mean planes of piperidine and pyrimidine rings is 49.57 (11)°. A short intra­molecular C—H⋯N contact generates an S(7) ring. In the crystal, N—H⋯N hydrogen bonds link the mol­ecules into (100) sheets and a weak aromatic π-π stacking inter­action is observed [centroid–centroid separation = 3.5559 (11) Å] between inversion-related pyrimidine rings.

The crystal structure of pirfenidone, C12H11NO [alternative name: 5-methyl-1-phenyl­pyridin-2(1H)-one], an active pharmaceutical ingredient (API) approved in Europe and Japan for the treatment of Idiopathic pulmonary fibrosis (IPF), is reported here for the first time. It was crystallized from toluene by the temperature gradient technique, and crystallizes in the chiral monoclinic space group P21. The phenyl and pyridone rings are inclined to each other by 50.30 (11)°. In the crystal, mol­ecules are linked by C–H⋯O hydrogen bonds involving the same acceptor atom, forming undulating layers lying parallel to the ab plane.

The crystal structure of the title mol­ecular complex, [Ag2{VO2F2}2(C13H17N3O2)4]·4H2O, supported by the heterofunctional ligand tr-ad-COOH [1-(1,2,4-triazol-4-yl)-3-carb­oxy­adamantane] is reported. Four 1,2,4-triazole groups of the ligand link two AgI atoms, as well as AgI and VV centres, forming the heterobimetallic coordination cluster {AgI2(VVO2F2)2(tr)4}. VV exists as a vanadium oxofluoride anion and possesses a distorted trigonal–bipyramidal coordination environment [VO2F2N]. A carb­oxy­lic acid functional group of the ligand stays in a neutral form and is involved in hydrogen bonding with solvent water mol­ecules and VO2F2− ions of adjacent mol­ecules. The extended hydrogen-bonding network is responsible for the crystal packing in the structure.

The synthesis and crystal structures of a series of 6-aryl­fuvlenes (fulvene is 5-methyl­idene­cyclo­penta-1,3-diene) with varying methyl­ation patterns on the 6-phenyl substituent are reported, namely 6-(3-methyl­phen­yl)-1,3-di­phenyl­fulvene (C25H20), 6-(4-methyl­phen­yl)-1,3-di­phenyl­fulvene (C25H20), 6-mesityl-3-di­phenyl­fulvene (C27H24) and 6-(2,3,4,5,6-penta­methyl­phen­yl)-1,3-di­phenyl­fulvene (C29H28). The bond lengths are typical of those observed in related fulvenes. A network of C—H⋯π ring inter­actions consolidates the packing in each structure.

The asymmetric unit of the title compound, C14H14O6, a monomeric compound of poly(butyl­ene 2,5-furandi­carboxyl­ate), consists of one half-mol­ecule, the whole all-trans mol­ecule being generated by an inversion centre. In the crystal, the mol­ecules are inter­connected via C—H⋯O inter­actions, forming a mol­ecular sheet parallel to (10overline{2}). The mol­ecular sheets are further linked by C—H⋯π inter­actions.

The title compound (systematic name: bis­{2-[4-(acet­yloxy)-1H-indol-3-yl]ethan-1-aminium} but-2-enedioate), 2C14H19N2O2+·C4H2O42−, has a single protonated psilacetin cation and one half of a fumarate dianion in the asymmetric unit. There are N—H⋯O hydrogen bonds between the ammonium H atoms and the fumarate O atoms, as well as N—H⋯O hydrogen bonds between the indole H atoms and the fumarate O atoms. The hydrogen bonds hold the ions together in infinite one-dimensional chains along [111].