The crystal structure of potassium (1S)-D-galactit-1-ylsulfonate

The structure of the crystalline addition product (1) formed between d-galactose and potassium bisulfite (potassium hydrogen sulfite) has been determined by X-ray diffraction analysis and compared with those structures reported for the related addition products from d-glucose and d-mannose. As with the latter two sulfonates, the d-galactose derived compound has an open-chain structure, with the carbon chain adopting a near planar zigzag conformation extending to the sulfur atom, similar to the d-mannose derivative but in contrast to the sickle conformation adopted by the d-glucose derivative. This last compound also differs in crystallising as a monohydrate. Inter-chain linking through cation coordination leads to a three dimensional network in the crystal.     

Modelling and refinement of the crystal structure of nucleoprotamine from Gibbula divaricata

The molecular structure of nucleoprotamine from Gibbula divaricata and its packing in oriented fibers has been modelled both to fit the X-ray diffraction pattern and to avoid steric compression. The representative model consists of 51 poly (dinucleotide) B-DNA helices with 51 poly(hexapeptide) chains associated with the major grooves. The prevailing peptide conformation is beta. The four arginine residues present are hydrogen-bonded to DNA phosphates while neutral peptides protrude into the minor grooves of neighboring nucleoprotamine molecules which are packed 2.61 nm apart in a screw-disordered, quasi-hexagonal lattice. This model reconciles a number of earlier, apparently conflicting experimental results and explains the remarkable stability of nucleoprotamines.     

Solubility and crystal structure of N-(1-deoxy-beta-D-fructopyranos-1-yl)-l-histidine monohydrate ('D-fructose-l-histidine')

Within a set of food-related Amadori compounds, crystalline N-(1-deoxy-beta-D-fructopyranos-1-yl)-l-histidine monohydrate (Fru-l-HisxH(2)O) has an unusually low solubility in water, which we determined as 0.21 g/100 g at 25 degrees C. The majority of the other fructose-amino acid conjugates have solubilities exceeding 100 g/100 g in water at this temperature. We report the crystal structure data on Fru-l-HisxH(2)O. The conformation of the carbohydrate is the normal (2)C(5) pyranose chair. Bond lengths and valence angles compare well with the average values from a number of pyranose structures. All hydroxyl and carboxyl oxygen atoms, all nitrogen atoms and the water molecule are involved in an extensive hydrogen bonding, which forms a network of infinite chains with small antidromic rings.     

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.     

Functional implications from the Cid1 poly(U) polymerase crystal structure

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Highlights? Our structure identifies the UTP-binding pocket of the Cid1 protein ? The atomic model suggests a central role for the helix 4 ? We suggest that the NRM loop is blocked after triphosphate recognition ? We identify several loops likely involved in the RNA primer association/stabilization     

Molecular and crystal structure of (1----3)-alpha-D-glucan triacetate.

A crystal and molecular structure for GTA I, the low temperature polymorph of (1----3)-alpha-D-glucan triacetate, is proposed on the basis of X-ray diffraction analysis of well-oriented films, combined with stereochemical model refinement. The unit cell is monoclinic with parameters a = 30.17 A, b = 17.42 A, c (fibre axis) = 12.11 A, and beta = 90 degrees C. The probable space group is P2(1) with b axis unique. Six molecular chains pass through the unit cell with alternating polarity and with three independent chains comprising the asymmetric unit. The chain axes are located in a hexagonal packing arrangement. The chain backbone conformation is a left-handed, three-fold helix, but all nine O(6) acetyl groups of the asymmetric unit are in non-equivalent rotational positions. The most probable structure is indicated by X-ray residuals R = 0.261 and R" = 0.283, based on 62 reflection intensities (41 observed and 21 unobserved).     

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.     

The crystal structure of alpha-chitin (poly-N-acetyl-D-glucosamine)

A detailed model for the crystal structure of the fibrous polysaccharide chitin is proposed. The structure determination has been carried out by using an optical analogue instrument which proved to be an adequate and rapid tool for the derivation of Fourier transforms, signs of amplitudes and the production of optical Fourier syntheses. The new model of chitin accounts properly for known chemical and physical properties, including the infrared absorption as well as for x-ray data, but because of the limited resolution of the diffraction patterns it can only be regarded as a good approximation. The stereochemical configuration of the polysaccharide chains has certain implications for the structure of cellulose.     

Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement

A critical evaluation of the performance of X-ray refinement protocols using various energy functions is presented using the bovine pancreatic trypsin inhibitor (BPTI) protein. The four potential energy functions we explored include: (1) fully quantum mechanical calculations; (2) one based on an incomplete molecular mechanics (MM) energy function employed in the Crystallography and NMR System (CNS) with empirical parameters developed by Engh and Huber (EH), which lacks electrostatic and attractive van der Waals terms; (3) one based on a complete MM energy function (AMBER ff99 parameter set); and (4) the same as 3, with the addition of a Generalized Born (GB) implicit solvation term. The R, R (free), real space R values of the refined structures and deviations from the original experimental structure were used to assess the relative performance. It was found that at 1 Angstrom resolution the physically based energy functions 1, 3, and 4 performed better than energy function 2, which we attribute to the better representation of key interactions, particularly electrostatics. The observed departures from the experimental structure were similar for the refinements with physically based energy functions and were smaller than the structure refined with EH. A test refinement was also performed with the reflections truncated at a high-resolution cutoff of 2.5 Angstrom and with random perturbations introduced into the initial coordinates, which showed that low-resolution refinements with physically based energy functions held the structure closer to the experimental structure solved at 1 Angstrom resolution than the EH-based refinements.     

Molecular and crystal structure of the regenerated form of (1----3)-alpha-D-mannan.

The crystal structure of the hydrated form of (1----3)-alpha-D-mannan, obtained by solid-state deacetylation of the partially O-acetylated mannan, was analyzed by combined X-ray diffraction and stereochemical-model refinement techniques. The structure crystallizes in a four-chain, monoclinic unit cell with parameters a = 11.33 A, b = 18.36 A, c (fiber repeat) = 8.25 A, and gamma = 101.75 degrees, and the most probable space group is P2(1). In the most probable structure the chain-backbone conformation is a two-fold helix, but with all four O-6 rotational positions nonequivalent. The chains pack with antiparallel polarity and are connected by pairs of intermolecular hydrogen bonds that form an infinite, zig-zag sheet. There are 16 water molecules in the unit cell, generally embedded between the sheets in crystallographic positions, providing additional hydrogen bonding and establishing a three-dimensional hydrogen-bond network in the crystal structure. The reliability of the structure analysis is indicated by the X-ray residual R" = 0.281, based on 98 hkl reflection intensities.     

Immunocytochemical localization and crystal structure of human frequenin (neuronal calcium sensor 1)

Frequenin, a member of a large family of myristoyl-switch calcium-binding proteins, functions as a calcium-ion sensor to modulate synaptic activity and secretion. We show that human frequenin colocalizes with ARF1 GTPase in COS-7 cells and occurs in similar cellular compartments as the phosphatidylinositol-4-OH kinase PI4Kbeta, the mammalian homolog of the yeast kinase PIK1. In addition, the crystal structure of unmyristoylated, calcium-bound human frequenin has been determined and refined to 1.9 A resolution. The overall fold of frequenin resembles those of neurocalcin and the photoreceptor, recoverin, of the same family, with two pairs of calcium-binding EF hands and three bound calcium ions. Despite the similarities, however, frequenin displays significant structural differences. A large conformational shift of the C-terminal region creates a wide hydrophobic crevice at the surface of frequenin. This crevice, which is unique to frequenin and distinct from the myristoyl-binding box of recoverin, may accommodate a yet unknown protein ligand.     

The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1)

Cyclophilins comprise one of the three classes of peptidylprolyl isomerases found in all eukaryotic and prokaryotic organisms, as well as viruses. Many of the 17 annotated human cyclophilins contain the catalytic domain in tandem with other domains, and many of the specific functions of a particular cyclophilin or its associated domains remain unknown. The structure of the isomerase domain from a spliceosome-associated cyclophilin, PPWD1 (peptidylprolyl isomerase containing WD40 repeat), has been solved to 1.65 A. In the crystal, the N-terminus of one isomerase domain is bound in the active site of a neighboring isomerase molecule in a manner analogous to substrate. NMR solution studies show that this sequence binds to the active site of the cyclophilin, but cannot be turned over by the enzyme. A pseudo-substrate immediately N-terminal to the cyclophilin domain in PPWD1 could have wider implications for the function of this cyclophilin in the spliceosome, where it is located in human cells.     

Bovine chymotrypsinogen A X-ray crystal structure analysis and refinement of a new crystal form at 1.8 A resolution

The X-ray structure of a new crystal form of chymotrypsinogen A grown from ethanol/water has been determined at 1.8 A resolution using Patterson search techniques. The crystals are of orthorhombic space group P212121 and contain two molecules in the asymmetric unit. Both independent molecules (referred to as A and B) have been crystallographically refined to a final R value of 0.173 with reflection data to 1.8 A resolution. Owing to different crystal contacts, both independent molecules show at various sites conformational differences, especially in segments 33-38, 142-153 and 215-222. If these three loops are omitted in a comparison, the root-mean-square (r.m.s.) deviation of the main-chain atoms of molecules A and B is 0.32 A. If segments 70-79, 143-152 and 215-221 are omitted, a comparison of either molecule A or molecule B with the chymotrypsinogen model of Freer et al. (1970) reveals an r.m.s. deviation of the alpha-carbon atoms of about 0.7 A. Compared with the active enzyme, four spatially adjacent peptide segments, in particular, are differently organized in the zymogen: the amino-terminal segment 11-19 runs in a rigid but strained conformation along the molecular surface due to the covalent linkage through Cys1; also segment 184-194 is in a rigid unique conformation due to several mutually stabilizing interactions with the amino-terminal segment; segment 216-222, which also lines the specificity pocket, adapts to different crystal contacts and exists in both chymotrypsinogen molecules in different, but defined conformations; in particular, disulfide bridge 191-220, which covalently links both latter segments, has opposite handedness in molecules A and B; finally, the autolysis loop 142 to 153 is organized in a variety of ways and in its terminal part is completely disordered. Thus, the allosteric activation domain (Huber & Bode, 1978) is organized in defined although different conformations in chymotrypsinogen molecules A and B, in contrast to trypsinogen, where all four homologous segments of the activation domain are disordered. This reflects the structural variability and deformability of the activation domain in serine proteinase proenzymes. If the aforementioned peptide segments are omitted, a comparison of our chymotrypsinogen models with gamma-chymotrypsin (Cohen et al., 1981) yields an r.m.s. deviation for alpha-carbon atoms of about 0.5 A. The residues of the "active site triad" are arranged similarly, but the oxyanion hole is lacking in chymotrypsinogen.(ABSTRACT TRUNCATED AT 400 WORDS)     

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.