co

Crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum

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.




co

Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport

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.




co

Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway

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.




co

Exploring the complex map of insulin polymorphism: a novel crystalline form in the presence of m-cresol

A novel monoclinic phase of human insulin co-crystallized with m-cresol was structurally characterized by means of powder and single-crystal X-ray diffraction.




co

Confidence maps: statistical inference of cryo-EM maps

The concept of statistical signal detection by controlling the false-discovery rate (FDR) to aid the atomic model interpretation of cryo-EM density maps is reviewed. The recommended usage of the FDR software tool is presented together with its successful integration into the CCP-EM suite.




co

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

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.




co

Crystal and solution structures of fragments of the human leucocyte common antigen-related protein

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.




co

Structure of P46, an immunodominant surface protein from Mycoplasma hyopneumoniae: interaction with a monoclonal antibody

Structures of the immunodominant protein P46 from M. hyopneumoniae has been determined by X-ray crystallography and it is shown that P46 can bind a diversity of oligosaccharides, particularly xylose, which exhibits a very high affinity for this protein. Structures of a monoclonal antibody, both alone and in complex with P46, that was raised against M. hyopnemoniae cells and specifically recognizes P46 are also reported.




co

Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins

The bond-valence method was performed on 51 crystal data sets from nitrogenase proteins, indicating the presence of molybdenum(III) in FeMo cofactors and vanadium(III) with more reduced iron complements in FeV cofactors.




co

Structure of ClpC1-NTD in complex with the anti-TB natural product ecumicin reveals unique binding interactions

Comparison of the structures of ClpC1-Ecumicin and ClpC1-Rufomycin reveals unique interaction relevant to the mode of action.




co

Structure of Thermococcus litoralis Δ1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline

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.




co

Di­chlorido­{N,N,N'-trimethyl-N'-(1H-pyrazol-1-yl-κN2)meth­yl]ethane-1,2-di­amine-κ2N,N'}copper(II) methanol monosolvate

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.




co

Bis[benzyl 2-(heptan-4-yl­idene)hydrazine-1-carboxyl­ate]bis­(thio­cyanato)­cobalt(II)

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.




co

Crystal structure of a salt with a protonated sugar cation and a cobalt(II) complex anion: (GlcN–H, K)[Co(NCS)4]·2H2O

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.




co

Bis(μ2-benzoato-κ2O,O')bis­(benzoato-κO)bis(ethanol-κO)bis­(μ3-hydroxido)hexa­kis­(μ-pyrazol­ato-κ2N,N')hexa­copper(II) ethanol disolvate

Trinuclear copper–pyrazolate entities are present in various Cu-based enzymes and nanojar supra­molecular arrangements. The reaction of copper(II) chloride with pyrazole (pzH) and sodium benzoate (benzNa) assisted by microwave radiation afforded a neutral centrosymmetric hexa­nuclear copper(II) complex, [Cu6(C7H5O2)4(OH)2(C3H3N2)6(C2H5OH)2]·2C2H5OH. Half a mol­ecule is present in the asymmetric unit that comprises a [Cu3(μ3-OH)(pz)3]2+ core with the copper(II) atoms arranged in an irregular triangle. The three copper(II) atoms are bridged by an O atom of the central hydroxyl group and by three bridging pyrazolate ligands on each of the sides. The carboxyl­ate groups show a chelating mode to one and a bridging syn,syn mode to the other two CuII atoms. The coordination environment of one CuII atom is square-planar while it is distorted square-pyramidal for the other two. Two ethanol mol­ecules are present in the asymmetric unit, one binding to one of the CuII atoms, one as a solvent mol­ecule. In the crystal, stabilization arises from inter­molecular O—H⋯O hydrogen-bonding inter­actions.




co

1:1 Co-crystal of 3-ethyl-4-methyl-3-pyrrolin-2-one and 3-ethyl-4-methyl-3-pyrroline-2,5-dione

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.




co

Synthesis and crystal structure of [Cs([2.2.2]crypt)]2[Mo(CO)5]

Reduction of the heteroleptic metal carbonyl complex Mo(CO)3(η5-Cp)H with the metallic salt Cs5Bi4 in the presence of [2.2.2]crypt (= 4,7,13,16,21,24-hexa­oxa-1,10-di­aza­bicyclo­[8.8.8]hexa­cosa­ne) in liquid ammonia led to single crystals of bis­[(4,7,13,16,21,24-hexa­oxa-1,10-di­aza­bicyclo­[8.8.8]hexa­cosa­ne)caesium] penta­carbonyl­molybdate, [Cs(C18H36N2O6)]2[Mo(CO)5] or [Cs([2.2.2]crypt)]2[Mo(CO)5]. The twofold negatively charged anionic complex corresponds to the 18 valence electron rule. It consists of an Mo atom coordinated by five carbonyl ligands in a shape inter­mediate between trigonal–bipyramidal and square-pyramidal. The Mo—C distances range from 1.961 (3) to 2.017 (3) Å, and the C≡O distances from 1.164 (3) to 1.180 (4) Å.




co

μ2-Methanol-κ2O:O-bis­[(1,10-phenanthroline-κ2N,N')bis­(2,3,4,5-tetra­fluoro­benzoato)-κO;κ2O,O'-copper(II)]

In the title compound, [Cu2(C7HF4O2)4(C12H8N2)2(CH3OH)], the mol­ecule lies on a twofold rotation axis in space group C2/c. The Cu2+ ion exhibits a distorted octa­hedral sphere with two N atoms from the phenanthroline ligand, three O atoms from the 2,3,4,5-tetra­fluoro­benzoate ligands and one O atom from a methanol mol­ecule. The distortion from an octa­hedral shape is a consequence of the Jahn–Teller effect of CuII and the small bite angle for the bidentate fluoro­benzoate ligand [54.50 (11)°]. The methanol mol­ecule bridges two symmetry-related CuII atoms to form the complete mol­ecule. In the bidentate fluoro­benzoate ligand, one F atom is disordered over two positions of equal occupancy. In the crystal structure, only weak inter­molecular inter­actions are observed.




co

Bis(1-dodecyl-4-aza-1-azoniabi­cyclo­[2.2.2]octane)tetra­iso­thio­cyanato­cobalt(II)

The title compound, [Co(C18H37N2)2(NCS)4], consists of a cobalt(II) ion positioned on the origin of the triclinic unit cell. It is coordinated by the N atoms of two trans-oriented 1-dodecyl-4-aza-1-azoniabi­cyclo­[2.2.2]octane (DABCO+) cations, which carry n-dodecyl chains at the non-coordinating N atoms. The distorted octa­hedral coordination environment of the CoII ion is completed through four N atoms of iso­thio­cyanate ions, which are arranged within the equatorial plane. Non-classical hydrogen bonding of the types C—H⋯N and C—H⋯S between the filamentous mol­ecules lead to the formation of layers parallel to (001).




co

Dicaesium tetra­magnesium penta­kis­(carbonate) deca­hydrate, Cs2Mg4(CO3)5·10H2O

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.




co

Poly[(μ4-5,7-di­hydro-1H,3H-dithieno[3,4-b:3',4'-e]pyrazine-κ4N:N':S:S')tetra-μ3-iodido-tetra­copper]: a three-dimensional copper(I) coordination polymer

The reaction of ligand 5,7-di­hydro-1H,3H-dithieno[3,4-b:3',4'-e]pyrazine (L) with CuI lead to the formation of a three-dimensional coordination polymer, incorporating the well known [CuxIx]n staircase motif (x = 4). These polymer [Cu4I4]n chains are linked via the N and S atoms of the ligand to form the three-dimensional coordination polymer poly[(μ4-5,7-di­hydro-1H,3H-dithieno[3,4-b:3',4'-e]pyrazine-κ4N:N':S:S')tetra-μ3-iodido-tetra­copper], [Cu4I4(C8H8N2S2)]n (I). The asymmetric unit is composed of half a ligand mol­ecule, with the pyrazine ring located about a center of symmetry, and two independent copper(I) atoms and two independent I− ions forming the staircase motif via centers of inversion symmetry. The framework is consolidated by C—H⋯I hydrogen bonds.




co

Diaquatetra­kis(μ-3-meth­oxy­benzoato-κ2O1:O1')dicopper(II)

The asymmetric unit of the binuclear title compound, [Cu2(C8H7O3)4(H2O)2], comprises two halves of diaquatetra­kis­(μ-3-meth­oxy­benzoato-κ2O1:O1')dicopper(II) units. The paddle-wheel structure of each complex is completed by application of inversion symmetry, with the inversion centre situated at the midpoint between two CuII atoms in each dimer. The two CuII atoms of each centrosymmetric dimer are bridged by four 3-meth­oxy­benzoate anions resulting in Cu⋯Cu separations of 2.5961 (11) and 2.6060 (12) Å, respectively. The square-pyramidal coordination sphere of each CuII atom is completed by an apical water mol­ecule. Inter­molecular O—H⋯O hydrogen bonds of weak nature link the complexes into layers parallel to (100). The three-dimensional network structure is accomplished by C—H⋯O hydrogen bonds inter­linking adjacent layers.




co

Poly[[μ4-3,4,8,10,11,13-hexa­hydro-1H,6H-bis­([1,4]di­thio­cino)[6,7-b:6',7'-e]pyrazine]di-μ-iodido-dicopper(I)]: a two-dimensional copper(I) coordination polymer

The reaction of ligand 3,4,8,10,11,13-hexa­hydro-1H,6H-bis­([1,4]di­thio­cino)[6,7-b:6',7'-e]pyrazine (L) with CuI led to the formation of a two-dimensional coordination polymer, incorporating a [Cu2I2] motif. These units are linked via the four S atoms of the ligand to form the title two-dimensional coordination poly­mer, poly[[μ4-3,4,8,10,11,13-hexa­hydro-1H,6H-bis­([1,4]di­thio­cino)[6,7-b:6',7'-e]pyrazine]di-μ-iodido-dicopper(I)], [Cu2I2(C12H16N2S4)]n, (I). The asymmetric unit is composed of a ligand mol­ecule, two copper(I) atoms and two I− ions. Both copper(I) atoms are fourfold S2I2 coordinate with almost regular trigonal-pyramidal environments. In the crystal, the layers, lying parallel to (102), are linked by C—H⋯I hydrogen bonds, forming a supra­molecular framework.