The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A

The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3',5'-bisphosphate (pdTp) has been refined by stereochemically restrained least-squares minimization to a crystallographic R value of 0.161 at 1.65 A resolution. The estimated root-mean-square (rms) error in the coordinates is 0.16 A. The final model comprises 1082 protein atoms, one calcium ion, the pdTp molecule, and 82 solvent water molecules; it displays an rms deviation from ideality of 0.017 A for bond distances and 1.8 degrees for bond angles. The mean distance between corresponding alpha carbons in the refined and unrefined structures is 0.6 A; we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket. The details of the calcium liganding and solvent structure in the active site are clearly shown in the final electron density map. The structure of the catalytic site is consistent with the mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that of enzyme and substrate.     

The structure of the aquaporin-1 water channel: a comparison between cryo-electron microscopy and X-ray crystallography

Three different medium-resolution structures of the human water channel aquaporin-1 (AQP1) have been solved by cryo-electron microscopy (cryo-EM) during the last two years. Recently, the structure of the strongly related bovine AQP1 was solved by X-ray crystallography at higher resolution, allowing a validation of the original medium-resolution structures, and providing a good indication for the strengths and limitations of state of the art cryo-EM methods. We present a detailed comparison between the different models, which shows that overall, the structures are highly similar, deviating less than 2.5 A from each other in the helical backbone regions. The two original cryo-EM structures, however, also show a number of significant deviations from the X-ray structure, both in the backbone positions of the transmembrane helices and in the location of the amino acid side-chains facing the pore. In contrast, the third cryo-EM structure that included information from the X-ray structure of the homologous bacterial glycerol facilitator GlpF and that was subsequently refined against cryo-EM AQP1 data, shows a root mean square deviation of 0.9A from the X-ray structure in the helical backbone regions.     

X-ray crystal structure of iridoid glucoside aucubin and its aglycone

X-ray diffraction analyses of iridoid glycoside aucubin (1) and its aglycone aucubigenin (2) are reported. It was found that crystals of 1 are orthorhombic, with P2₁2₁2₁ space group, both cyclopentane ring and pyran ring adopt envelope conformations, and the Glc moiety is in the ⁴C₁ conformation. Crystals of 2 are monoclinic, with space group P2₁, the cyclopentane and pyran rings also adopt the envelope conformation. The absolute configurations of 1 and 2 were also determined. Intensive O–HO hydrogen bonds in both crystal lattices were observed.     

Deamination of 1-aminoethylferrocene and the crystal structure of ethenylferrocene

Ethenylferrocene, C₁₂H₁₂Fe, was an unexpected product of the thermolysis of 1-aminoethylferrocene in a melt reaction with naphthalene-2,3-dicarboxylic acid. It was characterized by single crystal X-ray diffraction which revealed that the cyclopentadiene rings are slightly staggered and the ethenyl substituent lies approximately in the plane of the substituted cyclopentadiene ring. In the crystal structure C–Hπ interactions link molecules into parallel rows.     

X-ray crystal structure and molecular dynamics simulation of bovine pancreas phospholipase A2–n-dodecylphosphorylcholine complex

The crystal structure of n-dodecylphosphorylcholine (n-C₁₂PC)–bovine pancreas phospholipase A₂ (PLA₂) complex provided the following structural.characteristics: (1) the dodecyl chain of n-C₁₂PC was located at the PLA₂ N -terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2-acyl fatty acid chain (β-chain) of the substrate phospholipid, (2) the region from Lys-53 to Lys-56 creates a cholinereceiving pocket of n-C₁₂PC and (3) the N-termillal group of Ala-1 shifts significantly toward the Tyr-52 OH group by the binding of the n-C1₂PC inhibitor. Since the accuracy of the X-ray analysis (R = 0.275 at 2.3 Å resolution) was insufficient to establish these important X-ray insights, the complex structure was further investigated through the molecular dynamics (M D) simulation, assuming a system in aqueous solution at 310K. The M D simulation covering 176 ps showed that the structural characteristics observed by X-ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the M D simulation made clear that the PLA₂ binding pocket is large enough to permit the conformational fluctuation of the n-C₁₂PC hydrocarbon chain. © 1994 Wiley-Liss, Inc. © 1994 Wiley-Liss, Inc.     

A model of insulin fibrils derived from the x-ray crystal structure of a monomeric insulin (despentapeptide insulin)

The crystal structure of despentapeptide insulin, a monomeric insulin, has been refined at 1.3 Å spacing and subsequently used to predict and model the organization in the insulin fibril. The model makes use of the contacts in the densely packed despentapeptide insulin crystal, and takes into account other experimental evidence, including binding studies with Congo red. The dimensions of this model fibril correspond well with those measured experimentally, and the monomer–monomer contacts within the fibril are in accordance with the known physical chemistry of insulin fibrils. Using this model, it may be possible to predict mutations in insulin that might alleviate problems associated with fibril formation during insulin therapy. © 1997 Wiley-Liss Inc.     

The X-ray crystal structure of human beta-hexosaminidase B provides new insights into Sandhoff disease

Human lysosomal beta-hexosaminidases are dimeric enzymes composed of alpha and beta-chains, encoded by the genes HEXA and HEXB. They occur in three isoforms, the homodimeric hexosaminidases B (betabeta) and S (alphaalpha), and the heterodimeric hexosaminidase A (alphabeta), where dimerization is required for catalytic activity. Allelic variations in the HEXA and HEXB genes cause the fatal inborn errors of metabolism Tay-Sachs disease and Sandhoff disease, respectively. Here, we present the crystal structure of a complex of human beta-hexosaminidase B with a transition state analogue inhibitor at 2.3A resolution (pdb 1o7a). On the basis of this structure and previous studies on related enzymes, a retaining double-displacement mechanism for glycosyl hydrolysis by beta-hexosaminidase B is proposed. In the dimer structure, which is derived from an analysis of crystal packing, most of the mutations causing late-onset Sandhoff disease reside near the dimer interface and are proposed to interfere with correct dimer formation. The structure reported here is a valid template also for the dimeric structures of beta-hexosaminidase A and S.     

X-ray structure of Glu 53 human lysozyme.

The three-dimensional structure of a modified human lysozyme (HL), Glu 53 HL, in which Asp 53 was replaced by Glu, has been determined at 1.77 A resolution by X-ray analysis. The backbone structure of Glu 53 HL is essentially the same as the structure of wild-type HL. The root mean square difference for the superposition of equivalent C alpha atoms is 0.141 A. Except for the Glu 53 residue, the structure of the active site region is largely conserved between Glu 53 HL and wild-type HL. However, the hydrogen bond network differs because of the small shift or rotation of side chain groups. The carboxyl group of Glu 53 points to the carboxyl group of Glu 35 with a distance of 4.7 A between the nearest carboxyl oxygen atoms. A water molecule links these carboxyl groups by a hydrogen bond bridge. The active site structure explains well the fact that the binding ability for substrates does not significantly differ between Glu 53 HL and wild-type HL. On the other hand, the positional and orientational change of the carboxyl group of the residue 53 caused by the mutation is considered to be responsible for the low catalytic activity (ca. 1%) of Glu 53 HL. The requirement of precise positioning for the carboxyl group suggests the possibility that the Glu 53 residue contributes more than a simple electrostatic stabilization of the intermediate in the catalysis reaction.     

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 crystal structure of staphylococcal nuclease refined at 1.7 A resolution

The crystal structure of staphylococcal nuclease has been determined to 1.7 A resolution with a final R-factor of 16.2% using stereochemically restrained Hendrickson-Konnert least-squares refinement. The structure reveals a number of conformational changes relative to the structure of the ternary complex of staphylococcal nuclease 1,2 bound with deoxythymidine-3',5'-diphosphate and Ca2+. Tyr-113 and Tyr-115, which pack against the nucleotide base in the nuclease complex, are rotated outward creating a more open binding pocket in the absence of nucleotide. The side chains of Ca2+ ligands Asp-21 and Asp-40 shift as does Glu-43, the proposed general base in the hydrolysis of the 5'-phosphodiester bond. The significance of some changes in the catalytic site is uncertain due to the intrusion of a symmetry related Lys-70 side chain which hydrogen bonds to both Asp-21 and Glu-43. The position of a flexible loop centered around residue 50 is altered, most likely due to conformational changes propagated from the Ca2+ site. The side chains of Arg-35, Lys-84, Tyr-85, and Arg-87, which hydrogen bond to the 3'- and 5'-phosphates of the nucleotide in the nuclease complex, are unchanged in conformation, with packing interactions with adjacent protein side chains sufficient to fix the geometry in the absence of ligand. The nuclease structure presented here, in combination with the stereochemically restrained refinement of the nuclease complex structure at 1.65 A, provides a wealth of structural information for the increasing number of studies using staphylococcal nuclease as a model system of protein structure and function.     

A solution thermodynamic study of the Cu(II) and Zn(II) complexes of EBTA: X-ray crystal structure of the dimeric complex [Cu2(EBTA)(H2O)3]2

The copper(II) complex of the acyclic EBTA ligand (H₄EBTA = 1,2-bis(2-aminoethoxy)benzene-N,N,N′,N′-tetraacetic acid) has been prepared and characterized by X-ray analysis. The two copper ions of the dinuclear unit present the same distorted octahedral coordination polyhedra. The EBTA ligand is shared between two copper coordination centres, with the formation of centrosymmetric dimers, which are linked in a supramolecular tridimensional structure via additional interactions through the coordinated waters molecules with adjacent carboxylic oxygen atoms. The stability and protonation constants of EBTA with Cu(II) and Zn(II) ions indicate a higher stability of these complexes with respect to the corresponding complexes with the more flexible EGTA ligand (H₄EGTA = ethyleneglycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid). On the other hand, the lower stability of [Gd(EBTA)]⁻ than [Gd(EGTA)]⁻ results in a decreased overall selectivity (lower K_sel) of EBTA towards Gd(III) and suggests that this complex may undergoes transmetallation reactions under physiological conditions.     

Crystallization and preliminary X-ray diffraction studies of peroxidase from a fungus Arthromyces ramosus

Peroxidase (donor: H₂O₂ oxi-doreductase [EC 1.11.1.7]) was purified from the culture broth of the hyphomycete Arthromyces ramosus in the early log phase to show a single band on SDS-PAGE. The crystals of A. ramosus peroxidase (ARP) were formed by salting out with ammonium sulfate at room temperature and pH 7.5. The repeated seeding technique was employed to grow the crystals to the size large enough for X-ray diffraction study. The crystals were characterized as tetragonal, space group P4₂2₁2, with unit cell dimensions of a = b = 74.5 Å, c = 117.6 Å. The asymmetric unit contains one molecule of peroxidase. They diffract X-rays to at least 2.0 Å resolution and are stable to X-rays. © 1993 Wiley-Liss, Inc.     

The Fe-heme structure of met-indoleamine 2,3-dioxygenase-2 determined by X-ray absorption fine structure

Multiple-scattering (MS) analysis of EXAFS data on met-indoleamine 2,3-dioxygenase-2 (IDO2) and analysis of XANES have provided the first direct structural information about the axial donor ligands of the iron center for this recently discovered protein. At 10 K, it exists in a low-spin bis(His) form with Fe–N_p(av) = 1.97 Å, the Fe–N_Im bond lengths of 2.11 Å and 2.05 Å, which is in equilibrium with a high-spin form at room temperature. The bond distances in the low-spin form are consistent with other low-spin hemeproteins, as is the XANES spectrum, which is closer to that of the low-spin met-Lb than that of the high-spin met-Mb. The potential physiological role of this spin equilibrium is discussed.     

Synthesis, X-ray crystal structure and magnetic study of a dicyanamido bridged 1D chain nickel(II) complex

Reaction of Ni(NO₃)₂ · 6H₂O and sodium dicyanamide (Nadca) yields a 1D infinite chain complex {[Ni(dien)(μ_1,5-dca)(H₂O)](NO₃)}_n (1) (where dien = diethylenetriamine). The coordination environment in complex 1 around the nickel(II) ions is distorted octahedron. Three nitrogen atoms of the ligand diethylenetriamine and an oxygen atom of H₂O molecule constitute the four coordination sites of the basal plane of the octahedron. Of two axial positions of the octahedron, one position is occupied by the nitrogen atom of a μ_1,5-dca anion the remaining coordination site is occupied by a nitrogen atom of another end-to-end bridging dca from an adjacent [Ni(dien)(μ_1,5-dca)(H₂O)] moiety, yielding 1D infinite chains which propagate parallel to crystallographic a-axis. No measurable magnetic interaction was evidenced through variable temperature magnetic susceptibility measurements (4-300 K). However, the magnetic susceptibility of the compound can be explained in terms of single-ion anisotropic model with zero-field splitting for nickel(II) ions.     

Synthesis and crystal structure of tetrameric silver(I) 3,5-di-tert-butyl-pyrazolate

A tetrameric [Ag(μ-3,5-^tBu₂pz)]₄ · CH₂Cl₂ (1 · CH₂Cl₂) has been prepared and structurally characterized. The four Ag-atoms are in an approximate rhombic arrangement with pyrazolato bridges alternating on either side of the Ag₄-plane. A ¹H NMR study shows partial decomposition of 1 to the mononuclear [Ag(3,5-^tBu₂pzH)₂]⁺ in solution.     

A new lectin family with structure similarity to actinoporins revealed by the crystal structure of Xerocomus chrysenteron lectin XCL

A newly defined family of fungal lectins displays no significant sequence similarity to any protein in the databases. These proteins, made of about 140 amino acid residues, have sequence identities ranging from 38% to 65% and share binding specificity to N-acetyl galactosamine. One member of this family, the lectin XCL from Xerocomus chrysenteron, induces drastic changes in the actin cytoskeleton after sugar binding at the cell surface and internalization, and has potent insecticidal activity. The crystal structure of XCL to 1.4 A resolution reveals the architecture of this new lectin family. The fold of the protein is not related to any of the several lectin folds documented so far. Unexpectedly, the structure similarity is significant with actinoporins, a family of pore-forming toxins. The specific structural features and sequence signatures in each protein family suggest a potential sugar binding site in XCL and a possible evolutionary relationship between these proteins. Finally, the tetrameric assembly of XCL reveals a complex network of protomer-protomer interfaces and generates a large, hydrated cavity of 1000 A3, which may become accessible to larger solutes after a small conformational change of the protein.     

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.     

The crystal structure at 2A resolution of the Ca2+ -binding protein S100P

S100P is a small calcium-binding protein of the S100 EF-hand-containing family of proteins. Elevated levels of its mRNA are reported to be associated with the progression to hormone independence and metastasis of prostate cancer and to be associated with loss of senescence in human breast epithelial cells in vitro. The first structure of human recombinant S100P in calcium-bound form is now reported at 2.0A resolution by X-ray diffraction. A flexible linker connects the two EF-hand motifs. The protein exists as a homodimer formed by non-covalent interactions between large hydrophobic areas on monomeric S100P. Experiments with an optical biosensor to study binding parameters of the S100P monomer interaction showed that the association rate constant was faster in the presence of calcium than in their absence, whereas the dissociation rate constant was independent of calcium. The K(d) values were 64(+/-24)nM and 2.5(+/-0.8) microM in the presence and in the absence of calcium ions, respectively. Dimerization of S100P is demonstrated in vivo using the yeast two-hybrid system. The effect of mutation of specific amino acids suggests that dimerization in vivo can be affected by amino acids on the dimer interface and in the hydrophobic core.     

Blue phosphorescent iridium complexes based on 2-(fluoro substituted phenyl)-4-methylpyridines: Synthesis, crystal structure, and photophysics

A series blue phosphorescent emitting materials based on 2-(fluoro substituted phenyl)-4-methylpyridine as the cyclometalated ligands have been synthesized and characterized. The complexes have the general structure (C^{^}N)₂Ir(pic), where C^{^}N is a monoanionic cyclometalating ligand (e.g., 2-(2,4-difluorophenyl)-4-methylpyridine (24f₂pmpyH), 2-(3,4-difluorophenyl)-4-methylpyridine (34f₂pmpyH), 2-(3,5-difluorophenyl)-4-methylpyridine (35f₂pmpyH), and 2-(3,4,5-trifluorophenyl)-4-methyl-pyridine (345f₃pmpyH)), pic is 2-picolinic acid. The absorption, emission, cyclic voltammetry and thermostability of the complexes were systematically investigated. The (46f₂pmpy)₂Ir(pic) has been characterized using X-ray crystallography and the electronic ground state calculated using B3LYP density functional theory. HOMO levels are a mixture of Ir and 2-(fluoro phenyl)-4-methylpyridine ligand orbitals, while the LUMO is predominantly pic ligand based. Introduction of fluorine atoms and methyl group into ppy ligand and changing in position of F substituents in phenyl ring can finely tune emission of the complexes, showing bright blue-to-green luminescence at a wavelength of 463-501 nm at room temperature in CH₂Cl₂.     

The crystal structure of annexin A8 is similar to that of annexin A3

Annexin A8 is a relatively infrequent and poorly studied member of this large family of calcium-binding and membrane-binding proteins. It is, however, associated with a specific disease, acute promyelocytic leukemia. We have solved its three-dimensional structure, which includes a moderately long and intact N terminus. The structure is closest to that of annexin A3 and highlights several important regions of inherent flexibility in the annexin molecule. The N terminus resembles that of annexin A3, as it lies along the concave surface of the molecule and inserts partially into the hydrophilic channel in its centre. Since both annexins A3 and A8 are expressed in promyelocytic cells during their differentiation, the similarity in their structures might suggest a functional relationship.