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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 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.

Chromatin is the complex assembly of nucleic acids and proteins that makes up the physiological form of the eukaryotic genome. The nucleosome is the fundamental repeating unit of chromatin, and is composed of ∼147 bp of DNA wrapped around a histone octamer formed by two copies of each core histone: H2A, H2B, H3 and H4. Prior to nucleosome assembly, and during histone eviction, histones are typically assembled into soluble H2A/H2B dimers and H3/H4 dimers and tetramers. A multitude of factors interact with soluble histone dimers and tetramers, including chaperones, importins, histone-modifying enzymes and chromatin-remodeling enzymes. It is still unclear how many of these proteins recognize soluble histones; therefore, there is a need for new structural tools to study non-nucleosomal histones. Here, a single-chain, tailless Xenopus H2A/H2B dimer was created by directly fusing the C-terminus of H2B to the N-terminus of H2A. It is shown that this construct (termed scH2BH2A) is readily expressed in bacteria and can be purified under non-denaturing conditions. A 1.31 Å resolution crystal structure of scH2BH2A shows that it adopts a conformation that is nearly identical to that of nucleosomal H2A/H2B. This new tool is likely to facilitate future structural studies of many H2A/H2B-interacting proteins.

The setup and operation of an industrial cryo-EM laboratory is described.

The crystal structure of the c-type cytochrome NirC from Pseudomonas aeruginosa has been determined and reveals the simultaneous presence of monomers and 3D domain-swapped dimers in the same asymmetric unit.

Key structural biology experiments that have sought to elucidate how potassium ions permeate and pass through the selectivity filter of potassium ion channels are reviewed.

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.

The crystal and solution SAXS structures of a fragment of human leucocyte common antigen-related protein show that it is less flexible than the homologous proteins tyrosine phosphatase receptors δ and σ.

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.

The structure of the title compound, C24H26S2, an example of a pincer ligand with an SCS-chelation motif, illustrates the steric effects of the methyl groups in the thio­phenyl rings at the 2- and 6-positions, forcing a dissimilar spatial orientation of the thio­phenyl rings relative to the central aryl group [dihedral angles = 33.58 (7) and 40.49 (7)°]. In the crystal, weak S⋯S contacts [3.4009 (7) Å] link the mol­ecules into inversion dimers.

In the title compound, [CuCl2(C9H18N4)]·CH3OH, the central CuII ion is coordinated by three N atoms from the pyrazole derivative ligand and two chloride co-ligands. The coordination geometry around the CuII ion is distorted trigonal–bipyramidal. In the crystal, the mol­ecules are linked by C—H⋯O, C—H⋯Cl and O—H⋯Cl hydrogen bonds, forming a three-dimensional framework with the lattice solvent mol­ecule.

In the complex cation of title compound, [Fe(C56H52N4)(C5H8N2)2]ClO4·1.5C6H5Cl, the ironIII atom is coordinated in a distorted octa­hedral manner by four pyrrole N atoms of the porphyrin ring system in the equatorial plane, and by two N atoms of the 1-ethyl­imidazole ligands in the axial sites. A disordered perchlorate anion and one and a half chloro­benzene solvent mol­ecules are also present. The cationic complex exhibits a highly ruffled porphyrin core. The average Fe—Np (Np is a porphyrin N atom) bond length is 1.988 (5), and the axial Fe—NIm (NIm is an imidazole N atom) bond lengths are 1.962 (3) and 1.976 (3) Å. The two 1-ethyl­imidazole ligands are inclined to each other by a dihedral angle of 68.62 (16)°. The dihedral angles between the 1-ethyl­imidazole planes and the planes of the closest Fe—Np vector are 28.52 (18) and 43.57 (13)°. Inter­molecular C—H⋯Cl inter­actions are observed.

The title compound, C13H10INO, is not planar as the dihedral angle between the planes of the two aryl rings is 44.5 (9)°. The configuration about the central C=N bond is E, and there is an intra­molecular O—H⋯N hydrogen bond which generates an S(6) ring. The mol­ecular packing is stabilized by weak C—H⋯π inter­actions. The structure was refined as a two-component inversion twin.

6-Methyluracil, C5H6N2O2, exists in two crystalline phases: form (I), monoclinic, space group P21/c [Reck et al. (1988). Acta Cryst. A44, 417–421] and form (II), monoclinic, space group C2/c [Leonidov et al. (1993). Russ. J. Phys. Chem. 67, 2220–2223]. The structure of polymorph (II) has been redetermined providing a significant increase in the precision of the derived geometric parameters. In the crystal, mol­ecules form ribbons approximately running parallel to the c-axis direction through N—H⋯O hydrogen bonds. The radical differences observed between the crystal packing of the two polymorphs may be responsible in form (II) for an increase in the contribution of the polar canonical forms C—(O−)=N—H+ relative to the neutral canonical form C(=O)—N—H induced by hydrogen-bonding inter­actions.

In the mol­ecule of the title N,N'-disubstituted imidazol-2-yl­idene palladium(II) complex, [PdBr2(C21H24N4O)]·CH2Cl2, the palladium(II) atom adopts a slightly distorted square-planar coordination (r.m.s. deviation = 0.0145 Å), and the five-membered chelate ring is almost planar [maximum displacement = 0.015 (8) Å]. The mol­ecular conformation is enforced by intra­molecular C—H⋯Br hydrogen bonds. In the crystal, complex mol­ecules and di­chloro­methane mol­ecules are linked into a three-dimensional network by C—H⋯O and C—H⋯Br hydrogen bonds.

The title compound, C13H30N+·Br− (systematic name: N,N,N-trimethyl-1-deca­naminium bromide), forms crystals having a bilayer structure, comprised of layers of tri­methyl­ammonium cations and bromide anions separated by the inter-digitated n-decyl groups of the cation; close ammonium-methyl-C—H⋯Br contacts connect the ions. The n-decyl chain adopts a slightly distorted all-trans conformation. The n-decyl chain exhibits positional disorder with all atoms at half occupancy. The sample was a racemic 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.

The asymmetric unit of the title sulfodi­imide, C22H22N2OS, consists of two crystallographically independent mol­ecules with similar conformations The environment around each sulfur atom is a slightly distorted tetra­hedron with two S=N bonds and two S—C bonds. The S= N(m-methyl­benzo­yl) and S=N(NEt) bond lengths are 1.584 (3) and 1.528 (2) Å, respectively, for one mol­ecule, and 1.575 (2) and 1.529 (3) Å, respectively, for the other. The dihedral angles between the two phenyl rings in the mol­ecules are 86.76 (8) and 82.49 (8)°. The N—S—N—C(m-methyl­benzo­yl) and N—S—N—C(eth­yl) torsion angles are −60.5 (2) and −50.28 (19)°, respectively, for one mol­ecule, and 62.9 (2) and 44.2 (3)°, respectively, for the other. In the crystal, each independent mol­ecule is linked to its inversion-related mol­ecule via a pair of C—H⋯O hydrogen bonds, forming a dimer.

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.

The title compound {systematic name: [2-(1H-indol-3-yl)eth­yl](meth­yl)propyl­amine}, C14H20N2, has a single mol­ecule in the asymmetric unit. The mol­ecules in the unit cell are held together in infinite one-dimensional chains along [010] through N—H⋯N hydrogen bonds between indole H atoms and tri­alkyl­amine N atoms.

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.

The asymmetric unit of the title compound (systematic name: 3,3,8,8-tetra­methyl-1,4,6,9-tetra­oxa-λ4-bora­spiro­[4.4]nonane-2,7-dione tetra­hydrate), C8H12BO6·4H2O, consists of half a bis­(2-methyl­lactato)borate mol­ecule and two water mol­ecules of solvation. In the crystal, O—H⋯O hydrogen bonds link the components into a three-dimensional network.

While the crystal structure analysis of the title compound, C26H38O15, a synthetic derivative of sucrose, was originally reported 40 years ago [Drew et al. (1979). Carbohydr. Res. 71, 35–42], the present work has allowed for the determination of its absolute configuration through the application of resonant scattering techniques.

The title compound, [Ag2(C2H3O2)2(C19H20N2)2] (2), was readily synthesized by treatment of 3-benzyl-1-(2,4,6-tri­methyl­phen­yl)imidazolium chloride with silver acetate. The solution structure of the complex was analyzed by NMR spectroscopy, while the solid-state structure was confirmed by single-crystal X-ray diffraction studies. Compound 2 crystallizes in the triclinic space group Poverline{1}, with a silver-to-carbene bond length (Ag—CNHC) of 2.084 (3) Å. The mol­ecule resides on an inversion center, so that only half of the mol­ecule is crystallographically unique. The planes defined by the two imidazole rings are parallel to each other, but not coplanar [inter­planar distance is 0.662 (19) Å]. The dihedral angles between the imidazole ring and the benzyl and mesityl rings are 77.87 (12) and 72.86 (11)°, respectively. The crystal structure features π–π stacking inter­actions between the benzylic groups of inversion-related (−x + 1, −y + 1, −z + 1) mol­ecules and C—H⋯π inter­actions.

Single crystals of the title complex, [Zn(C7H5N2O4)2(C2H6OS)2] or [Zn(NBZH)2(DMSO)2], were isolated from a dimethyl sulfoxide (DMSO) solution containing [Zn(NBZH)2]·2H2O (NBZH = 3-nitro­benzo­hydroxamate anion). The asymmetric unit comprises of one O,O'-chelating NBZH anion, one O-bound DMSO ligand and one zinc(II) cation localized on an inversion centre. The three-dimensional crystal packing includes N—H⋯O and C—H⋯O hydrogen bonding, as well as O⋯H and H⋯H contacts identified by Hirshfeld isosurface analysis.

The title complex, [RuCl(C10H14)(C10H8N2)](C24H20B), has monoclinic (P21) symmetry at 100 K. It was prepared by the reaction of the di­chlor­ido[1-methyl-4-(propan-2-yl)benzene]­ruthenium(II) dimer with 2,2'-bi­pyridine, followed by the addition of ammonium tetra­phenyl­borate. The 1-methyl-4-(propan-2-yl)benzene group, the 2,2'-bi­pyridine unit and a chloride ion coordinate the ruthenium(II) atom, with the 1-methyl-4-(propan-2-yl)benzene ring and bi­pyridine moieties trans to each other. In the crystal, the complex cations are linked by C—H⋯Cl hydrogen bonds, forming chains parallel to [010]. These chains are linked by a number of C—H⋯π inter­actions, involving the phenyl rings of the tetra­phenyl­borate anion and a pyridine ring of the bpy ligand, resulting in the formation of layers parallel to (10overline{1}).

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.

The complete mol­ecule of the title compound, C32H22F12N4O2, is generated by a crystallographic twofold axis aligned parallel to [010]. The F atoms of one of the CF3 groups are disordered over three orientations in a 0.6: 0.2: 0.2 ratio. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, forming zigzag chains propagating along the a-axis direction. In addition, weak C—H⋯O and C—H⋯F bonds are observed. The contribution of the disordered solvent to the scattering was removed using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] of PLATON. The solvent contribution is not included in the reported mol­ecular weight and density.

The title compound, C31H30O6, was obtained by protecting the six hy­droxy groups of apogossypol by acetalization with di­chloro­methane. The mol­ecule has a bridging dioxepine unit which hinders the rotation around the 2,2'-inter­naphthyl bond. The dihedral angle between the naphthyl units is 55.73 (3)°. In the crystal, very weak C—H⋯O inter­actions may help to consolidate the packing.

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 salt, C24H27N2OS+·BF4−, was prepared by an alkyl­ation at the amino N atom attached to the sulfur atom of the corresponding sulfodi­imide. The configuration around the sulfur atom is a slightly distorted tetra­hedral geometry with two S—N bonds and two S—C bonds. The lengths of the S—N(di­ethyl­amine) and S=N(m-methyl­benzoyl­imine) bonds are 1.619 (2) and 1.551 (2) Å, respectively. The two N—S—N—C(eth­yl) and the N—S—N—C(m-methyl­benzoyl­imine) torsion angles are −85.43 (3), 58.94 (17) and 62.03 (16)°, respectively. The dihedral angle between the two phenyl rings is 84.03 (14)°. In the crystal, C—H⋯F hydrogen bonds link the cation and anion, forming a three-dimensional network.

In the title compound, C16H16Cl2N2O2S, the pyrazole ring has an envelope conformation with the C atom bearing the phenyl ring being the flap. The dihedral angles between the central pyrazole ring (all atoms) and pendant thio­phene and phenyl rings are 2.00 (14) and 81.49 (12)°, respectively. In the crystal, weak C—H⋯O, Cl⋯π and π–π stacking inter­actions link the mol­ecules into a three-dimensional network.

Crystallization from a 20-year-old commercial source of 3-ethyl-4-methyl-3-pyrrolin-2-one afforded 1:1 co-crystals of this compound (C7H11NO) with its oxidized derivative, 3-ethyl-4-methyl-3-pyrroline-2,5-dione (C7H9NO2). The compound crystallizes in the space group Poverline{1}, with two mol­ecules of each species in the asymmetric unit. These four mol­ecules form a hydrogen-bonded tetra­mer with a dimer of 3-ethyl-4-methyl-3-pyrrolin-2-one as the core flanked by one mol­ecule of the dione on each side.

In the title compound, C34H35NO4, the dihedral angle between the pyridine ring and attached benzene ring is 79.17 (8)°. The meth­oxy­eth­oxy–eth­oxy side chain is disordered over two orientations in a 0.732 (7):0.268 (7) ratio. In the crystal, very weak C—H⋯N and C—H⋯O inter­actions link the mol­ecules.

In the cation of the title mol­ecular salt, C15H19N2+·PF6−, the dihedral angle between the benzene and pyridine rings is 38.21 (10)°. In the crystal, weak C—H⋯F inter­actions arising from methyl and methyl­ene groups adjacent to the quaternary N atom generate (001) sheets.

The asymmetric unit of the title compound, C17H20O5, contains two independent mol­ecules, A and B, with similar geometries [dihedral angles between the phenyl rings = 56.19 (8) and 54.98 (7)°, respectively]. Intra­molecular O—H⋯O hydrogen bonds occur in both mol­ecules. In the crystal, the A mol­ecules form [1overline{1}0] chains linked by O—H⋯O hydrogen bonds from the hydroxyl group to one of the meth­oxy O atoms. The B mol­ecules form O—H⋯O hydrogen bonds to the hydroxyl O atoms of the A mol­ecules and thus act as fixed spacers between the chains of mol­ecule A. Some weak C—H⋯O contacts are also present.

The solid-state structural analysis of the title compound [systematic name: 5,11-disulfanylidene-4,6,10,12-tetrakis(2,4,6-trimethylphenyl)-4,6,10,12-tetraazatricyclo[7.3.0.03,7]dodeca-1(9),3(7)-diene-2,8-dione], C44H44N4O2S2 [+solvent], reveals that the mol­ecule crystallizes in a highly symmetric cubic space group so that one quarter of the mol­ecule is crystallographically unique, the mol­ecule lying on special positions (two mirror planes, two twofold axes and a center of inversion). The crystal structure exhibits large cavities of 193 Å3 accounting for 7.3% of the total unit-cell volume. These cavities contain residual density peaks but it was not possible to unambiguously identify the solvent therein. The contribution of the disordered solvent mol­ecules to the scattering was removed using a solvent mask and is not included in the reported mol­ecular weight. No classical hydrogen bonds are observed between the main mol­ecules.

In the title compound, C21H18O4, the dihedral angle between the naphthelene ring system (r.m.s. deviation = 0.014 Å) and the benzene ring is 9.68 (1)°. The C atom of the meth­oxy group of the naphthalene ring system is almost coplanar with the ring [C—O—C—C = −2.0 (3)°], whereas the C atom of the meth­oxy group of the phenol ring is slightly twisted [C—O—C—C = 6.2 (3)°]. An intra­molecular O—H⋯O hydrogen bond generates an S(6) ring motif.

The title compound, C16H16N2O6, lies about an inversion centre at the mid-point of the N—N bond. The mol­ecule features two intra­molecular O—H⋯N and two C—H⋯O hydrogen bonds, each of which forms an S(6) ring motif. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds into infinite zigzag chains propagating along the c-axis direction. π–π stacking inter­actions between the pyrone rings [centroid–centroid distances = 3.975 (2) Å] stack the mol­ecules along b.