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.     

Solvothermal synthesis, crystal structure and luminescence of the first organic amine templated europium sulfate

The first organic amine templated europium sulfate [C₂N₂H₁₀]_1.5[Eu(SO₄)₃(H₂O)] · 2H₂O (1), has been synthesized under solvothermal conditions by using a mixture of n-butanol and water as the solvent. The colorless block crystals were characterized by IR, TGA and ICP. Crystal structure analysis shows that the corrugated layered framework of compound 1 is constructed from EuO₉ polyhedra and sulfate groups, while non-coordination water molecules and ethylenediamine molecules link the adjacent layers by hydrogen bonds. Compound 1 represents a strong luminescence upon the excitation.     

‘Tennis Rackets for Octopodes’ - the crystal and molecular structure of a novel triphosphorus-containing trication

The novel trication [1,4,7-tris(diphenylphosphonium)norbornane] has been isolated as its tris(tetrachloroaluminate) salt 1, and its crystal and molecular structure established by single-crystal X-ray diffraction at 120 K.     

The crystal structure of a cyclic glycolipid reveals a carbohydrate-carbohydrate interaction interface

The crystal structure of an amphiphilic macrocycle [Velasco-Torrijos, T.; Murphy, P. V., Tetrahedron: Asymmetry2005, 16, 261-272] derived from saccharides shows extensive hydrogen-bonding networks, including participation of water, that may have relevance for the modelling of carbohydrate-carbohydrate recognition at cell-cell interfaces. The structure may provide a basis for understanding the binding of the macrocycle to hydrophobic probes.     

The crystal structure of the 1:1 inclusion complex of beta-cyclodextrin with benzamide

The 1:1 inclusion complex of beta-cyclodextrin and benzamide was prepared and characterized by single crystal X-ray diffraction, PXRD, TGA, and IR. This complex crystallizes in the monoclinic P2(1) space group with unit cell constants a=15.4244(16), b=10.1574(11), c=20.557(2)A, beta=110.074(2) degrees , V=3025.1(6)A(3). The guest molecule projects into the beta-cyclodextrin cavity from the primary hydroxyl side. The amide group protrudes from the primary hydroxyl side and forms hydrogen bonds with the adjacent beta-cyclodextrin molecule. There are six crystallized water molecules, which play crucial roles in crystal packing.     

Ultra-high resolution crystal structure of a dimeric defensin SPE10

Defensins are key players of the innate immune system known to act against bacteria, fungi and viruses. Here we report the 0.98-Å crystal structure of SPE10, a dimeric plant defensin. SPE10 associates as a dimer through a unique amino acid triplet involving residues R36–W42–R40. The helix from one subunit interacts with arginines R36 and R40 from the other subunit, forming a sheet-like dimer with a highly extended molecular surface. A conserved hydrophobic patch on the molecular head largely overlaps with the putative receptor-binding site previously reported for another defensin. Structural analysis and mutational studies indicate that the dimeric association of SPE10 is relevant to its function, and that the hydrophobic patch on the molecular head is required for its antifungal activity.

Structured summary

SPE10binds to SPE10 by X-ray crystallography(View interaction)     

The crystal structure of Arabidopsis thaliana RAC7/ROP9: the first RAS superfamily GTPase from the plant kingdom

Arabidopsis thaliana RAC/ROP GTPases constitute a plant specific Rho GTPase family in the RAS superfamily, which has been implicated in numerous pivotal signalling cascades in plants. Research has shown that plants in some cases have evolved different modes of regulating Rho GTPase activity as compared to the equivalent systems in animals and yeast. In order to gain structural insight into plant signaling at the molecular level, we have determined the first crystal structure of a RAC-like GTPase belonging to the RAS superfamily from the plant kingdom. The structure of AtRAC7/ROP9 bound to GDP was solved at a resolution of 1.78 A. We have found that the structure of plant Rho GTPases is based upon a conserved G-domain architecture, but structural differences were found concerning the insert region and switch II region of the protein.     

The crystal structure of the small GTPase Rab11b reveals critical differences relative to the Rab11a isoform

Rab GTPases constitute the largest family of small monomeric GTPases, including over 60 members in humans. These GTPases share conserved residues related to nucleotide binding and hydrolysis, and main sequence divergences lie in the carboxyl termini. They cycle between inactive (GDP-bound) and active (GTP-bound) forms and the active site regions, termed Switch I and II, undergo the larger conformational changes between the two states. The Rab11 subfamily members, comprising Rab11a, Rab11b, and Rab25, act in recycling of proteins from the endosomes to the plasma membrane, in transport of molecules from the trans-Golgi network to the plasma membrane and in phagocytosis. In this work, we describe Rab11b-GDP and Rab11b-GppNHp crystal structures solved to 1.55 and 1.95 angstroms resolution, respectively. Although Rab11b shares 90% amino acid identity to Rab11a, its crystal structure shows critical differences relative to previously reported Rab11a structures. Inactive Rab11a formed dimers with unusually ordered Switch regions and missing the magnesium ion at the nucleotide binding site. In this work, inactive Rab11b crystallized as a monomer showing a flexible Switch I and a magnesium ion which is coordinated by four water molecules, the phosphate beta of GDP (beta-P) and the invariant S25. S20 from the P-loop and S42 from the Switch I are associated to GTP hydrolysis rate. In the active structures, S20 interacts with the gamma-P oxygen in Rab11b-GppNHp but does not in Rab11a-GppNHp and the Q70 side chain is found in different positions. In the Rab11a-GTPgammaS structure, S40 is closer to S25 and S42 does not interact with the gamma-P oxygen. These differences indicate that the Rab11 isoforms may possess different GTP hydrolysis rates. In addition, the Switch II of inactive Rab11b presents a 3(10)-helix (residues 69-73) that disappears upon activation. This 3(10)-helix is not found in the Rab11a-GDP structure, which possesses a longer alpha2 helix, spanning from residue 73 to 82 alpha-helix 5.     

The crystal structure of a novel phosphopantothenate synthetase from the hyperthermophilic archaea, Thermococcus onnurineus NA1

Pantothenate is the essential precursor of coenzyme A (CoA), a fundamental cofactor in all aspects of metabolism. In bacteria and eukaryotes, pantothenate synthetase (PS) catalyzes the last step in the pantothenate biosynthetic pathway, and pantothenate kinase (PanK) phosphorylates pantothenate for its entry into the CoA biosynthetic pathway. However, genes encoding PS and PanK have not been identified in archaeal genomes. Recently, a comparative genomic analysis and the identification and characterization of two novel archaea-specific enzymes show that archaeal pantoate kinase (PoK) and phosphopantothenate synthetase (PPS) represent counterparts to the PS/PanK pathway in bacteria and eukaryotes. The TON1374 protein from Thermococcus onnurineus NA1 is a PPS, that shares 54% sequence identity with the first reported archaeal PPS candidate, MM2281, from Methanosarcina mazei and 91% sequence identity with TK1686, the PPS from Thermococcus kodakarensis. Here, we report the apo and ATP-complex structures of TON1374 and discuss the substrate-binding mode and reaction mechanism.     

The first crystal structure of a phospholipase D

BACKGROUND: The phospholipase D (PLD) superfamily includes enzymes that are involved in phospholipid metabolism, nucleases, toxins and virus envelope proteins of unknown function. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. PLD also catalyses a transphosphatidylation reaction in the presence of phosphatidylcholine and a short-chained primary or secondary alcohol. RESULTS: The first crystal structure of a 54 kDa PLD has been determined to 1.9 A resolution using the multiwavelength anomalous dispersion (MAD) method on a single WO(4) ion and refined to 1.4 A resolution. PLD from the bacterial source Streptomyces sp. strain PMF consists of a single polypeptide chain that is folded into two domains. An active site is located at the interface between these domains. The presented structure supports the proposed superfamily relationship with the published structure of the 16 kDa endonuclease from Salmonella typhimurium. CONCLUSIONS: The structure of PLD provides insight into the structure and mode of action of not only bacterial, plant and mammalian PLDs, but also of a variety of enzymes as diverse as cardiolipin synthases, phosphatidylserine synthases, toxins, endonucleases, as well as poxvirus envelope proteins having a so far unknown function. The common features of these enzymes are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.     

Synthesis and crystal structure of a novel three-dimensional supramolecular network containing one-dimensional honeycomb-like channels

A novel supramolecular assembly containing honeycomb-like channels [Cu(mal)(bpy)] · 3H₂O (mal = malate, bpy = 2,2′-bipy) has been synthesized and characterized by elemental analyses, IR, EPR, TG, UV-Vis and single crystal X-ray diffraction. Compound 1 is constructed from spiral-shaped chains via O-H?O hydrogen bonds and π-π stacking interactions. To our knowledge, compound 1 represents the first supramolecular network constructed from the mixed malate and pyridine ligand.     

Hydrothermal synthesis, crystal structure and physical properties of a new gadolinium phosphite hydrate

A new compound Gd₄(H₂O)₅(HPO₃)₆ (1) was isolated from the reaction of gadolinium chloride GdCl₃ · nH₂O with H₃PO₃ under hydrothermal conditions. The crystal structure was solved by means of single-crystal X-ray diffraction. The structure is composed of parallel gadolinium-oxygen polyhedra chains connected by phosphite ions, and shows three-dimensional (3D) open-framework with eight-membered ring (8MR) channels. The structure is different from its counterpart Eu₂(H₂O)_2.5(PO₃H)₃ due to the effect of lanthanide contraction. The intensive intrinsic UV emission of this compound at λ_max = 312 nm comes from the spin-forbidden ⁶P_7/2 → ⁸S_7/2 f-f transition of the Gd³⁺ ions. No magnetic order was observed for this compound.     

1.42 Å crystal structure of mini-IGF-1(2): an analysis of the disulfide isomerization property and receptor binding property of IGF-1 based on the three-dimensional structure

Insulin and insulin-like growth factor 1 (IGF-1) share a homologous sequence, a similar three-dimensional structure and weakly overlapping biological activity, but IGF-1 folds into two thermodynamically stable disulfide isomers, while insulin folds into one unique stable tertiary structure. This is a very interesting phenomenon in which one amino acid sequence encodes two three-dimensional structures, and its molecular mechanism has remained unclear for a long time. In this study, the crystal structure of mini-IGF-1(2), a disulfide isomer of an artificial analog of IGF-1, was solved by the SAD/SIRAS method using our in-house X-ray source. Evidence was found in the structure showing that the intra-A-chain/domain disulfide bond of some molecules was broken; thus, it was proposed that disulfide isomerization begins with the breakdown of this disulfide bond. Furthermore, based on the structural comparison of IGF-1 and insulin, a new assumption was made that in insulin the several hydrogen bonds formed between the N-terminal region of the B-chain and the intra-A-chain disulfide region of the A-chain are the main reason for the stability of the intra-A-chain disulfide bond and for the prevention of disulfide isomerization, while Phe B1 and His B5 are very important for the formation of these hydrogen bonds. Moreover, the receptor binding property of IGF-1 was analyzed in detail based on the structural comparison of mini-IGF-1(2), native IGF-1, and small mini-IGF-1.     

Synthesis, crystal structure and electroluminescent properties of a Schiff base zinc complex

A new complex of zinc with a Schiff base, zinc(N,N′-bis(salicylidene)-3, 6-dioxa-1, 8-diaminooctane monohydrate) (ZnBSO · H₂O), was synthesized and characterized by means of elemental analyses, IR spectra and DTA-TG. Its structure was determined by X-ray single crystal analysis. It was demonstrated that the zinc atom is coordinated by the two oxygen atoms in phenolate and two nitrogen atoms in imine of the ligand in a slightly distorted tetrahedral geometry, while the two oxygen atoms from the oxa-alkyl chain are not coordinated to Zn(II) atom. The energy levels of the HOMO, LUMO and the electrochemical band gap were determined by cyclic voltammeter. The electroluminescent devices with the complex as the emitter showed bright blue emission with a peak at 450 nm, which is same as the fluorescence of the complex in both solution and solid states.     

The first crystal structure of a Mimosoideae lectin reveals a novel quaternary arrangement of a widespread domain

The crystal structures of the apo and mannose-bound Parkia platycephala seed lectin represent the first structure of a Mimosoideae lectin and a novel circular arrangement of beta-prism domains, and highlight the adaptability of the beta-prism fold as a building block in the evolution of plant lectins. The P.platycephala lectin is a dimer both in solution and in the crystals. Mannose binding to each of the three homologous carbohydrate-recognition domains of the lectin occurs through different modes, and restrains the flexibility of surface-exposed loops and residues involved in carbohydrate recognition. The planar array of carbohydrate-binding sites on the rim of the toroid-shaped structure of the P.platycephala lectin dimer immediately suggests a mechanism to promote multivalent interactions leading to cross-linking of carbohydrate ligands as part of the host strategy against phytopredators and pathogens. The cyclic structure of the P.platycephala lectin points to the convergent evolution of a structural principle for the construction of lectins involved in host defense or in attacking other organisms.     

Synthesis, crystal structure and magnetism of a new mixed germanium-polyoxovanadate cluster

A new germanium-polyoxovanadate, (H₃aep)₄[V₁₄Ge₈O₅₀]·2(aep)·13H₂O (1), has been synthesized under solvothermal conditions applying GeO₂, NH₄VO₃, Cu(NO₃)₂·3H₂O and an aqueous solution of 1-(2-aminoethyl)-piperazine (aep, C₆H₁₈N₃) in the temperature range from 110 to 150 °C. The compound crystallizes in the non-centrosymmetric tetragonal space group P-42₁c with a = 17.193(1) Å, c = 16.501(1) Å, V = 4877.9(5) Å³ and Z = 2. The structure consists of isolated spherical [V^IV₁₄Ge^IV₈O₅₀]¹²⁻ cluster anions and protonated amine molecules as counterions. The cluster anion can be viewed as a derivative of the [V₁₈O₄₂] archetype by replacing four VO₅ pyramids by four Ge₂O₇ units. The latter are formed by corner-sharing of two [GeO₄]⁴⁻ tetrahedra. At temperatures above 150 °C the compound (H₂pip)₄(Hpip)₄[V^IV₁₄Ge^IV₈O₅₀(H₂O)] (2) (pip = piperazine, C₄N₂H₁₀) is formed and during the reaction Cu²⁺ is reduced to elemental copper. This redox reaction is essential for the formation of 2. The crystal water molecules in the structure of 1 are emitted at low temperatures. The magnetic properties are dominated by strong intra-cluster antiferromagnetic coupling and the strongest exchange between edge- and corner-sharing VO₅ square pyramids results in an eight-membered spin ring to which two three-membered spin bridges are joined. The magnetic susceptibility data suggest that even at the low temperature of 2 K several multiplet states are still significantly populated.     

Formation and crystal structure of bis-(2,2,6,6-tetramethylpiperidino)diselane

The reaction of N-lithioselenido-2,2,6,6-tetramethylpiperidine and trimethyltin chloride leads to the formation of hexamethyldistannane and bis-(2,2,6,6-tetramethyl-piperidino)diselane. This compound was identified by ¹H and ¹³C NMR, by mass spectrometry and elemental analysis. The crystal structure was also determined showing a conformation differing from other diaminodiselanes due to the repulsion of the bulky 2,2,6,6-tetramethyl-piperidino groups.     

Synthesis, crystal structure, and properties of two sandwich-type tungstovanadates

Two dimeric tungstovanadates of the form [M₄(H₂O)₂(VW₉O₃₄)₂]¹⁰⁻ (M = Mn^II, Co^II) were synthesized and characterized by elemental analysis, thermogravimetric analysis and infrared spectroscopy. X-ray single crystal analysis revealed that the two polyanion clusters with isomorphic structure consist of two lacunary [VW₉O₃₄]⁹⁻ Keggin moieties linked by four Mn^II or Co^II ions, forming a sandwich-type structure. The temperature-dependent magnetic susceptibility measurements showed a dominant antiferromagnetic interaction in complex 1, while ferromagnetic interactions were found in complex 2. The electrochemical behaviors of complexes 1 and 2 were investigated in buffer solution at pH 4.8. Surface photovoltage spectroscopy (SPS) and electric field-induced SPS (EFISPS) revealed that complex 1 bears the behavior of an n-type semiconductor, while complex 2 shows no obvious signal.     

Synthesis, crystal structure and esterification of a novel iron(III) 18-metallacrown-6 complex

The trianionic heptadentate ligand, (Z)-3-(5′-chlorosalicylhydrazinocarbonyl) propenoic acid, has been synthesized and reacted with FeCl₃·6H₂O, to produce the complex [Fe^III₆(C₁₂H₈N₂O₅Cl)₆(H₂O)₄(CH₃OH)₂]·8H₂O·4CH₃OH. In the self-assembly process the ligand was esterified and transferred into (Z)-methyl 3-(5′-chlorosalicylhydrazinocarbonyl) propenoate. In the crystal structure, the neutral Fe(III) complex contain a 18-membered metallacrown ring consisting of six Fe(III) and six trianionic ligands. The 18-membered metallacrown ring is formed by the succession of six structural moieties of the type [Fe(III)-N-N]. Due to the meridional coordination of the ligands to the Fe³⁺ ions, the ligands enforce the stereochemistry of the Fe³⁺ ions as a propeller configuration with alternating Λ/Δ forms. The metallacrown can be treated with SnCl₂ or Zn powder to obtain purified ester.