X-ray crystal structure and properties of tris(tetrathiafulvalenium) hexachloroplatinate

The title salt has been prepared by the diffusion of tetrathiafulvalene (TTF) and [NBuⁿ₄]₂[PtCl₆] in acetonitrile. Crystals (black plates) are tetragonal, space group P4/mbm, with a=11.757(2), c=11.707(2) Å, and Z=2. The block-diagonal least-squares refinement, based on 804 independent reflections with ∣F_o∣> 3σ(F), yields an R factor of 0.11. The structure is comprised of TTF-trimer units which are arranged perpendicularly to each other, forming a two-dimensional layer with somewhat close sulfur- sulfur contact among the trimers. The salt exhibits the electrical resistivity of 87 Ω cm as a compacted pellet at 25 °C. Binding energies of platinum 4f electrons of the [PtCl₆]²⁻ anion suggest an extreme reduction from the platinum(IV) state.     

X-ray crystal structure of galabiose, O-alpha-D-galactopyranosyl-(1---4)-D-galactopyranose

O-alpha-D-Galactopyranosyl-(1---4)-D-galactopyranose, C12H22O11, Mr = 342.30, crystallises in the orthorhombic space group P2(1)2(1)2(1), and has alpha = 5.826(1), b = 13.904(3), c = 17.772(4) A, Z = 4, and Dx = 1.579 g.cm-3. Intensity data were collected with a CAD4 diffractometer. The structure was solved by direct methods and refined to R = 0.063 and Rw = 0.084 for 2758 independent reflections. The glycosidic linkage is of the type 1-axial-4-axial with torsion angles phi O-5' (O-5'-C-1'-O-1'-C-4) = 98.1(2) degrees, psi C-3 (C-3-C-4-O-1'-C-1') = -81.9(3) degrees, phi H (H-1'-C-1'-O-1'-C-4) = -18 degrees, and psi H (H-4-C-4-O-1'-C-1') = 35 degrees. The conformation is stabilised by an O-3 . . . O-5' intramolecular hydrogen-bond with length 2.787(3) A and O-3-H . . . O-5' = 162 degrees. The glycosidic linkage causes a folding of the molecule with an angle of 117 degrees between the least-square planes through the pyranosidic rings. The crystal investigated contained 56(1)% of alpha- and 44(1)% of beta-galabiose as well as approximately 70% of the gauche-trans and approximately 30% of the trans-gauche conformers about the exocyclic C-5'-C-6' and C-5-C-6 bonds. The crystal packing is governed by hydrogen bonding that engages all oxygen atoms except the intramolecular acceptor O-5' and the glycosidic O-1' oxygen atoms.     

Palladium(II) complexes of 1,10-phenanthroline: Synthesis and X-ray crystal structure determination

Two palladium(II) complexes, [Pd(phen)(NCCH₃)₂][O₃SCF₃]₂ (1) and [Pd(phen)(μ-OH)]₂[O₃SCF₃]₂ · 2H₂O (2) (where phen = 1,10-phenanthroline), have been crystallized following the reaction of Pd(phen)Cl₂ with silver triflate, Ag(O₃SCF₃), in acetonitrile and water, respectively. The structures of both complexes are based on a Pd(phen)²⁺ metal core, with two acetonitrile molecules binding in a monodentate fashion in complex 1 and two hydroxo bridges holding together two cores to form a dimer in complex 2. Additionally, both complexes present a hydrogen bonded 3-D network involving the triflate anions in 1, and water and triflate anions in 2. Both complexes have been characterized by infrared and ¹H NMR spectroscopy and their crystal structures determined by X-ray crystallography.     

The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A.

The crystal structures of concanavalin A in complex with Man(alpha1-6)Man(alpha1-O)Me and Man(alpha1-3)Man(alpha1-O)Me were determined at resolutions of 2.0 and 2.8 A, respectively. In both structures, the O-1-linked mannose binds in the conserved monosaccharide-binding site. The O-3-linked mannose of Man(alpha1-3)Man(alpha1-O)Me binds in the hydrophobic subsite formed by Tyr-12, Tyr-100, and Leu-99. The shielding of a hydrophobic surface is consistent with the associated large heat capacity change. The O-6-linked mannose of Man(alpha1-6)Man(alpha1-O)Me binds in the same subsite formed by Tyr-12 and Asp-16 as the reducing mannose of the highly specific trimannose Man(alpha1-3)[Man(alpha1-6)]Man(alpha1-O)Me. However, it is much less tightly bound. Its O-2 hydroxyl makes no hydrogen bond with the conserved water 1. Water 1 is present in all the sugar-containing concanavalin A structures and increases the complementarity between the protein-binding surface and the sugar, but is not necessarily a hydrogen-bonding partner. A water analysis of the carbohydrate-binding site revealed a conserved water molecule replacing O-4 on the alpha1-3-linked arm of the trimannose. No such water is found for the reducing or O-6-linked mannose. Our data indicate that the central mannose of Man(alpha1-3)[Man(alpha1-6)]Man(alpha1-O)Me primarily functions as a hinge between the two outer subsites.     

The crystal and molecular structure of cyclo-[-(D-Val-Hyi-Val-D-Hyi)3-] (meso-valinomycin,C60H102N6O18)

The crystal structure of the valinomycin analog, cyclo-[(-D -Val-Hyi-Val-D -Hyi-)₃-] (meso-valinomycin, C₆₀H₁₀₂N₆O₁₈) has been determined by direct x-ray diffraction procedures. The crystals are triclinic, space group P1 , number of molecules per unit cell Z = 1, and cell parameters a = 11.831, b = 13.815, c = 14.889 Å, α = 109.54°, β = 116.10°, γ = 98.89°. The atomic coordinates for the C,N,O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation to R = 0.07. The structure is centrosymmetric and has a threefold axis of pseudosymmetry. The depsipeptide chain is in the form of a bracelet stabilized by six identical intramolecular 4 → 1 hydrogen bonds between the amide C?O and NH groups. The ester carbonyls are oriented towards the symmetry axis, their O atoms forming an ellipsoidal molecular cavity. The isopropyl side chains are located on the molecular periphery. The structure found differs considerably from the conformation of the crystalline naturally occurring antibiotic, valinomycin, but completely resembles that of valinomycin and meso-valinomycin in nonpolar solvents. In the crystal, meso-valinomycin molecules form stacks. The molecular cavities situated in the stacks one above the other along the pseudo-C₃ axis form a continuous channel, the internal surface of which is lined by O atoms. The possible conformations of depsipeptides of the valinomycin series and their mode of action in membranes are discussed in the light of the data obtained.     

The crystal structure of N(10)-formyltetrahydrofolate synthetase from Moorella thermoacetica

The structure was solved at 2.5 A resolution using multiwavelength anomalous dispersion (MAD) scattering by Se-Met residues. The subunit of N(10)-formyltetrahydrofolate synthetase is composed of three domains organized around three mixed beta-sheets. There are two cavities between adjacent domains. One of them was identified as the nucleotide binding site by homology modeling. The large domain contains a seven-stranded beta-sheet surrounded by helices on both sides. The second domain contains a five-stranded beta-sheet with two alpha-helices packed on one side while the other two are a wall of the active site cavity. The third domain contains a four-stranded beta-sheet forming a half-barrel. The concave side is covered by two helices while the convex side is another wall of the large cavity. Arg 97 is likely involved in formyl phosphate binding. The tetrameric molecule is relatively flat with the shape of the letter X, and the active sites are located at the end of the subunits far from the subunit interface.     

C(alpha)-hydroxymethyl methionine: synthesis, optical resolution and crystal structure of its (+)-N(alpha)-benzoyl derivative.

(R, S)-Methionine was transformed into C(alpha)-hydroxymethyl methionine by a route involving C(alpha)-hydroxymethylation of 2-phenyl-4-methylthioethyl-5-oxo-4,5-dihydro-1,3-oxazole. The absolute configuration of (-)-C(alpha)-hydroxymethyl methionine was elucidated to be (S) by chemical correlation with (S) (-)-C(alpha)-ethyl serine. Absolute structure determination (by single crystal X-ray diffraction) on N(alpha)-benzoyl-C(alpha)-hydroxymethyl methionine confirmed the (R)-configuration for the (+)-enantiomer. In addition, the X-ray diffraction analysis showed that the C(alpha,alpha)-disubstituted glycyl residue adopts the fully extended (C5) conformation.     

The crystal structure of N 6 -( 2 -isopentenyl)-2-methylthioadenine, a modified base of tRNA with cytokinin activity

The crystal structure of the title compound, a modified base of tRNA has been determined from three-dimensional x-ray diffraction data. The plane of the isopentenyl side chain is rotated 91° from the plane through the adenine system and the methyl thio group. The substituents on the adenine ring prevent N(1) from hydrogen bonding; the molecule exhibits instead two types of pairing arrangements, one of which is compatible with the Hoogsteen or “reversed” Hoogsteen pairing scheme.     

X-ray crystal structure of Staphylococcus aureus FemA

The latter stages of peptidoglycan biosynthesis in Staphylococci involve the synthesis of a pentaglycine bridge on the epsilon amino group of the pentapeptide lysine side chain. Genetic and biochemical evidence suggest that sequential addition of these glycines is catalyzed by three homologous enzymes, FemX (FmhB), FemA, and FemB. The first protein structure from this family, Staphylococcus aureus FemA, has been solved at 2.1 A resolution by X-ray crystallography. The FemA structure reveals a unique organization of several known protein folds involved in peptide and tRNA binding. The surface of the protein also reveals an L-shaped channel suitable for a peptidoglycan substrate. Analysis of the structural features of this enzyme provides clues to the mechanism of action of S. aureus FemA.     

The X-ray crystal structure of 2,5-anhydro-l-iditol

The crystal and molecular structure of 2,5-anhydro-l-iditol (1) has been determined by X-ray diffraction using direct methods to a final residual value of R = 0.051 for 1151 reflections. The crystals of 1 are orthorhombic, space group P2₁2₁2₁, a = 739.9 (4), b = 902.0 (5), c = 1109.1 (6) pm, with four molecules in the unit cell. In the crystal, the molecule does not show the expected C₂ symmetry: the ring CO bonds differ in length (145.0 vs. 143.6 pm) and the conformation of the tetrahydrofuran ring deviates slightly from the ideal ³T₄(l) arrangement (puckering parameters Q = 39.9 pm, Phi = 95.5°). Molecules are interlinked by a network of strong intermolecular hydrogen-bonding involving all hydroxyl groups. Except for O-3, all oxygen atoms act as acceptors in this pattern.     

X-ray crystal structure of Mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase II (mtKasB)

Mycolic acids are long chain alpha-alkyl branched, beta-hydroxy fatty acids that represent a characteristic component of the Mycobacterium tuberculosis cell wall. Through their covalent attachment to peptidoglycan via an arabinogalactan polysaccharide, they provide the basis for an essential outer envelope membrane. Mycobacteria possess two fatty acid synthases (FAS); FAS-I carries out de novo synthesis of fatty acids while FAS-II is considered to elongate medium chain length fatty acyl primers to provide long chain (C(56)) precursors of mycolic acids. Here we report the crystal structure of Mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase (ACP) II mtKasB, a mycobacterial elongation condensing enzyme involved in FAS-II. This enzyme, along with the M. tuberculosis beta-ketoacyl ACP synthase I mtKasA, catalyzes the Claisen-type condensation reaction responsible for fatty acyl elongation in FAS-II and are potential targets for development of novel anti-tubercular drugs. The crystal structure refined to 2.4 A resolution revealed that, like other KAS-II enzymes, mtKasB adopts a thiolase fold but contains unique structural features in the capping region that may be crucial to its preference for longer fatty acyl chains than its counterparts from other bacteria. Modeling of mtKasA using the mtKasB structure as a template predicts the overall structures to be almost identical, but a larger entrance to the active site tunnel is envisaged that might contribute to the greater sensitivity of mtKasA to the inhibitor thiolactomycin (TLM). Modeling of TLM binding in mtKasB shows that the drug fits the active site poorly and results of enzyme inhibition assays using TLM analogues are wholly consistent with our structural observations. Consequently, the structure described here further highlights the potential of TLM as an anti-tubercular lead compound and will aid further exploration of the TLM scaffold towards the design of novel compounds, which inhibit mycobacterial KAS enzymes more effectively.     

Nickel(II) and zinc(II) dimonensinates: Single crystal X-ray structure, spectral properties and bactericidal activity

Mononuclear transition metal complexes of the polyether ionophorous antibiotic monensin (monensic acid, MonH) with nickel(II) and zinc(II) were prepared and characterized using single crystal X-ray diffraction and spectral methods. Monensin complexes crystallize as [Ni(Mon)₂(H₂O)₂]·H₂O·5MeCN (1) and [Zn(Mon)₂(H₂O)₂]·H₂O·4.5MeCN (2), respectively, in the monoclinic space group P2₁. Compounds 1 and 2 consist of two monoanionic monensic acid ligands (monensinates) bound in a bidentate coordination mode to the transition metal ion. The metal center is placed in an octahedral environment with monensin anions occupying the equatorial plane of complexes via oxygens of carboxylate and hydroxyl groups located at the both ends of ionophore molecule. The strongly folded antibiotic anions are supported by intramolecular H-bonds, most of them originating from the two aqua ligands attached to the metal(II) ions in axial positions and completing their 6-fold coordination. The bioactivity assay reveals that the presence of divalent metal ion in the monensin complexes influences the biological properties of the ligand and should be taken into account when discussing its mode of action.     

Gas phase assembly and X-ray crystal structure of copper(I) 3,5-bis(trifluoromethyl)benzoate network with corannulene

Gas-phase co-deposition of [Cu(O₂C(3,5-CF₃)₂C₆H₃)] (1) with C₂₀H₁₀ at 170 °C affords crystals of the first copper(I)-corannulene adduct [Cu₆(O₂C(3,5-CF₃)₂C₆H₃)₆](C₂₀H₁₀)₂ (2). The X-ray crystallographic characterization of 2 reveals its main structural building blocks: a planar hexanuclear metal core supported by bridging 3,5-bis(trifluoromethyl)benzoate groups and two corannulene molecules. The Cu?Cu distances within the core of 2.6826(8)-2.7607(8) Å fall within the range of cuprophilic interactions. Several intermolecular Cu?C contacts between the cyclic Cu₆-unit and corannulene ranging from 2.799(5) to 3.266(5) Å can be identified. The shortest ones lying within the sum of the van der Waals radii for Cu and C (Σr_vdW (Cu, C) = 3.10 Å) are to the rim sites of corannulene. A noticeable flattening of the C₂₀H₁₀-bowl in 2 is also observed.     

Preparation and crystal structure of the recombinant alpha(1)/alpha(2) catalytic heterodimer of bovine brain platelet-activating factor acetylhydrolase Ib

The intracellular form of mammalian platelet activating factor acetylhydrolase found in brain (PAF-AH Ib) is thought to play a critical role in control in neuronal migration during cortex development. This oligomeric complex consists of a homodimer of the 45 kDa (beta) LIS1 protein, the product of the causative gene for type I lissencephaly, and, depending on the developmental stage and species, one of three possible pairs of two homologous approximately 26 kDa alpha-subunits, which harbor all of the catalytic activity. The exact composition of this complex depends on the expression patterns of the alpha(1) and alpha(2) genes, exhibiting tissue specificity and developmental control. All three possible dimers (alpha(1)/alpha(1), alpha(1)/alpha(2) and alpha(2)/alpha(2)) were identified in tissues. The alpha(1)/alpha(2) heterodimer is thought to play an important role in fetal brain. The structure of the alpha(1)/alpha(1) homodimer was solved earlier in our laboratory at 1.7 A. We report here the preparation of recombinant alpha(1)/alpha(2) heterodimers using a specially constructed bi-cistronic expression vector. The approach may be useful in studies of other systems where pure heterodimers of recombinant proteins are required. The alpha(1)/alpha(2) dimer has been crystallized and its structure was solved at 2.1 A resolution by molecular replacement. These results set the stage for a detailed characterization of the PAF-AH Ib complex.     

Amine free crystal structure: the crystal structure of d(CGCGCG)2 and methylamine complex crystal

We succeeded in the crystallization of d(CGCGCG)2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2Fo-Fc map was much clear and easily traced. It is the first time monoamine co-crystallizes with d(CGCGCG)2. However, methylamine was not found from the complex crystal of d(CGCGCG)2 and methylamine. Five Mg ions were found around d(CGCGCG)2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg2+. DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG)2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this.     

The X-ray crystal structure of full-length human plasminogen

Plasminogen is the proenzyme precursor of the primary fibrinolytic protease plasmin. Circulating plasminogen, which comprises a Pan-apple (PAp) domain, five kringle domains (KR1-5), and a serine protease (SP) domain, adopts a closed, activation-resistant conformation. The kringle domains mediate interactions with fibrin clots and cell-surface receptors. These interactions trigger plasminogen to adopt an open form that can be cleaved and converted to plasmin by tissue-type and urokinase-type plasminogen activators. Here, the structure of closed plasminogen reveals that the PAp and SP domains, together with chloride ions, maintain the closed conformation through interactions with the kringle array. Differences in glycosylation alter the position of KR3, although in all structures the loop cleaved by plasminogen activators is inaccessible. The ligand-binding site of KR1 is exposed and likely governs proenzyme recruitment to targets. Furthermore, analysis of our structure suggests that KR5 peeling away from the PAp domain may initiate plasminogen conformational change.     

Synthesis,reactivity, and X-ray crystal structure of a remarkably stable bis(alkoxo)platinum complex

Platinum complexes of the ligand Ph₂PCH₂CMe₂OH are described including [Pt(PPh₂CH₂CMe₂O)₂] which contains PtO bonds of unprecedented stability that readily undergo insertion of SO₂ and CO.