X-ray studies on crystalline complexes involving amino acids and peptides. XXIV. Different ionization states and novel aggregation patterns in the complexes of succinic acid with DL-and L-histidine

Diffusion of acetonitrile into an aqueous solution of DL -histidine and succinic acid in 1:3 molar proportions results in the crystals of DL -histidine hemisuccinate dihydrate [triclinic, P1 , a = 7.654(1), b = 8.723(1), c = 9.260(1) Å, α = 77.23(1), β = 72.37(1) and γ = 82.32 (1)°]. The replacement of DL -histidine by L -histidine in the crystallization experiment under identical conditions leads to crystals of L -histidine semisuccinate trihydrate [orthorhombic, P2₁2₁2₁, a = 7.030 (1), b = 8.773 (1), and c = 24.332 (3) Å]. The structures were solved using counter data and refined to R values of 0.056 and 0.054 for 2356 and 1778 observed reflections, respectively. Histidine molecules in both the complexes exist in open conformation I. Succinate and semisuccinate ions in them are planar, and exactly or nearly centrosymmetric. In the DL -histidine complex, the amino acid molecules form double ribbons and the succinate ions occupy voids left behind when the double ribbons aggregate, as in inclusion compounds. In the L -histidine complex, the amino acid molecules form columns; so do the semisuccinate ions and water molecules. The two columns interdigitate to form the complex crystal. There are similarities between the molecular aggregation in the complexes and that in the crystals of L - and DL -histidine. However, the presence of succinic acid has the effect of disrupting, partially or totally, head-to-tail sequences involving amino acid molecules. © 1993 John Wiley & Sons, Inc.     

X-ray studies on crystalline complexes involving amino acids and peptides: Part XVIII. Crystal structure of a new form of L-arginine D-glutamate and a comparative study of amino acid crystal structures containing molecules of the same and mixed chirality

The new form of L-arginine D-glutamate is monoclinic, P2₁, witha = 9.941(1),b = 4.668(2),c = 17.307(1) Å,β = 95.27(1)°, and Z = 2. In terms of composition, the new form differs from the old form in that the former is a monohydrate whereas the latter is a trihydrate. The structure has been solved by the direct methods and refined to R = 0.085 for 1012 observed reflections. The conformation of the arginine molecule is the same in both the forms whereas that of the glutamate ion is different. The change in the conformation of the glutamate ion is such that it facilitates extensive pseudosymmetry in the crystals. The molecules arrange themselves in double-layers stabilised by head-to-tail sequences involving main chains, in both the forms. However, considerable differences exist between the two forms in the interface, consisting of side chains and water molecules, between double-layers. A comparative study of the relationship between the crystal structures of L and DL amino acids on the one hand and that between the structures of LL and LD amino acid-amino acid complexes on the other, provides interesting insights into amino acid aggregation and the effect of chirality on it. The crystal structures of most hydrophobic amino acids are made up of double-layers and those of most hydrophilic amino acids contain single layers, irrespective of the chiralities of the amino acids involved. In most cases, the molecules tend to appropriately rearrange themselves to preserve the broad features of aggregation patterns when the chirality of half the molecules is reversed as in the structures of DL amino acids. The basic elements of aggregation in the LL and the LD complexes, are similar to those found in the crystals of L and DL amino acids. However, the differences between the LL and the LD complexes in the distribution of these elements are more pronounced than those between the distributions in the structures of L and DL amino acids.     

X-ray studies on crystalline complexes involving amino acids and peptides. Part XX. Crystal structures of DL-arginine acetate monohydrate and DL-lysine acetate and a comparison with the corresponding L-amino acid complexes

Crystals of DL-arginine acetate monohydrate, C6H15N4O2+C2H3O2-.H2O, are monoclinic, P2(1)/c, with a = 13.552(2), b = 5.048(2), c = 18.837(3) A, beta = 101.34(2) degrees and Z = 4, and those of DL-lysine acetate, C6H15N2O2+.C2H3O2- are triclinic, P1, with a = 5.471(2), b = 7.656(2), c = 12.841(2) A, alpha = 94.48(1), beta = 94.59(2), gamma = 98.83(2) degrees and Z = 2. The structures have been solved by direct methods and refined to R = 0.058 and 0.077 for 1522 and 1259 observed reflections respectively. The difference in the number and the nature of proton donors leads to a difference in hydrogen bond density in the two structures. The basic elements of aggregation in both the structures are pairs of amino acid molecules, each pair stabilized by two centrosymmetrically related hydrogen bonds involving alpha-amino and alpha-carboxylate groups, stacked along the shortest dimension to form columns. The pairs are held together in each column by head-to-tail sequences. The columns stack along a crystallographic axis to form layers. Adjacent layers are bridged by acetate ions. The amino acid-acetate interactions are primarily through side chains and involve specific interactions and characteristic interaction patterns. The gross features of molecular aggregation are nearly the same in DL-arginine acetate monohydrate and L-arginine acetate whereas they are substantially different in the lysine complexes. In both cases, one of the two head-to-tail sequences in the L complex is replaced by a hydrogen bonded loop involving alpha-amino and alpha-carboxylate groups, in the DL complex. This may have implications for prebiotic condensation during chemical evolution.     

Crystal and molecular structure of bis(tricyclohexylphosphine)silver(I)nitrate and bis(tricyclohexylphosphine)silver(I)perchlorate; correlation of the structures with the silver-phosphorus coupling constants

Two (1:2) silver monophosphine complexes have been studied by X-ray diffraction methods and in solution by P NMR spectroscopy. Both are monomeric and tricoordinated in the solid state but one of them, the perchlorate compound, is probably associated as a dimer species in solution from the lower ¹J(¹⁰⁷Ag³¹P) value when compared to the nitrate analogue. Previous structural correlations found in other silver-phosphine complexes have been confirmed for these new compounds. Thus, larger PAgP bond angles are associated with shorter AgP bond distances, longer Aganion bond distances and lower Lewis basicity of the anions. Selected structural data are: PAgP bond angle of 139.04(9)°, AgP bond lengths of 2.440(3) and 2.445(3) Å for the nitrate complex and 147.34(3)°, 2.429(1) Å and 2.432(1) Å, for the perchlorate one. J(¹⁰⁷Ag³¹P) is 457 Hz and 447 Hz, respectively. The complexes are triclinic, Z = 2, with the parameters: a = 9.258(2), b = 9.828(2), c = 23.385(5) Å, α = 94.73(2)°, β = 96.35(2)°, γ = 116.42(1)° (nitrate) and a = 9.505(2), b = 9.790(2), c = 23.667(6) Å, α= 99.03(2) β = 95.44(2) γ = 115.97(1)° (perchlorate).     

Purification,characterization, crystallization,and preliminary X-ray results from Paracoccus denitrificans porin

The porin from Paracoccus denitrificans ATCC 13543 was purified and crystallized. Two crystal forms were obtained from porin solutions with β-d-octylglucopyra-noside as detergent. Crystals of form I belong to the monoclinic spacegroup C2 with unit cell dimensions a = 112.2 Å, b = 193.8 Å, c = 100.5 Å and β = 129.2°. There is 1 trimer per asymmetric unit. Crystals of form II are triclinic with α = 89.7 Å, b = 98.8 Å, c = 112.5 Å, b = 112.5Å, β = 101.8°, γ = 106.7° (2 trimers per asymmetric unit). Both crystal forms diffract to 3 Å. © 1995 Wiley-Liss, Inc.     

Crystallization and characterization of the recombinant human Clara cell 10-kDa protein

Crystals of recombinant human Clara cell 10-kDa protein were grown both from ammonium sulfate and polyethylene glycol (PEG) solutions. Crystals grown from ammonium sulfate solution have been characterized by X-ray diffraction studies as monoclinic with the space group C2 and lattice constants a = 69.2 Å, b = 83.0 Å, c = 58.3 Å, and β = 99.7°. The monoclinic crystals diffract to beyond 2.5 Å. Some of the crystals grown from PEG were of a similar habit to those grown from ammonium sulfate, but others were triclinic with the space group P1 and cell constants a = 40.3 Å, b = 46.3 Å, c = 51.3 Å, α = 117.7°, β = 102.3°, and γ = 71.4°. These crystals diffract to beyond 3.2 Å. © 1994 Wiley-Liss, Inc.     

Crystallization of Thermus thermophilus histidyl-tRNA synthetase and Its complex with tRNAHis

Histidyl-tRNA synthetase (HisRS) has been purified from the extreme thermophile Thermus thermophilus. The protein has been crystallized separately with histidine and with its cognate tRNA^His. Both crystals have been obtained using the vapor diffusion method with ammonium sulphate as precipitant. The crystals of HisRS with histidine belong to the spacegroup P2₁2₁2 with cell parameters a = 171.3 Å, b = 214.7 Å, c = 49.3 Å, α = β = γ = 90°. A complete data set to a resolution of 2.7Å with an R_merge on intensities of 4.1% has been collected on a single frozen crystal. A partial data set collected on a crystal of HisRS in complex with tRNA_His shows that the crystals are tetragonal with cell parameters a = b = 232 Å, c = 559 Å, α = β = γ = 90° and diffract to about 4.5 Å resolution. © 1995 Wiley-Liss, Inc.     

Purification,crystallization, and preliminary crystallographic analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli

The phenylalanine-regulated isozyme of 3-deoxy-D-arabino-heptulosonate-7-phosphate- synthase (DAHPS) from Escherichia coli, its binary complexes with either substrate, phosphoenolpyruvate (PEP), or feedback inhibitor, Phe, and its ternary complexes with either PEP or Phe plus metal cofactor (either Mn²⁺, Cd²⁺, or Pb²⁺) were crystallized from polyethylglycol (PEG) solutions. All crystals of the DAHPS without Phe belong to space group C2, with cell parameters a = 213.5 Å, b = 54.3 Å, c = 149.0 Å, β = 116.6°. All crystals of the enzyme with Phe also belong to space group C2, but with cell parameters a = 297.1 Å, b = 91.4 Å, c = 256.5 Å, and β = 148.2°.     

Crystallization and preliminary X-ray diffraction studies of dogfish C-reactive protein

Crystals of dogfish (Mustelus canis) C-reactive protein were obtained through vapor phase equilibration using the sitting drop rod technique with ammonium sulfate as the precipitating agent. The space group was determined to be P1 (triclinic lattice) with unit cell dimensions of a = 82.91, b = 92.25 and c = 103.40 Å; α = 83.36°, β = 89.76°, and γ = 81.30°. These crystals diffract to about 2.6 Å resolution and contain two hexamers in the asymmetric unit. © 1993 Wiley-Liss, Inc.     

Visualization of Drug-Nucleic Acid Interactions at Atomic Resolution. IX. Structures of Two N,N-Dimethylproflavine: 5-Iodocytidylyl (3′-5′) Guanosine Crystalline Complexes

Abstract

This paper describes two complexes containing N,N-dimethylproflavine and the dinucleoside monophosphate, 5-iodocytidylyl(3′-5′)guanosine (iodoCpG). The first complex is triclinic, space group PI, with unit cell dimensions a = 11.78 Å, b = 14.55 Å, c = 15.50 Å, a = 89.2°, β = 86.2°, γ = 96.4°. The second complex is monoclinic, space group P2₁, with a = 14.20 Å, b = 19.00 Å, c = 20.73 Å, β = 103.6°. Both structures have been solved to atomic resolution and refined by Fourier and least squares methods. The first structure has been refined anisotropically to a residual of 0.09 on 5,025 observed reflections using block diagonal least squares, while the second structure has been refined isotropically to a residual of 0.13 on 2,888 reflections with full matrix least squares. The asymmetric unit in both structures contains two dimethylproflavine molecules and two iodoCpG molecules; the first structure has 16 water molecules (a total of 134 non-hydrogen atoms), while the second structure has 18 water molecules (a total of 136 non-hydrogen atoms). Both structures demonstrate intercalation of dimethylproflavine between base-paired iodoCpG dimers. In addition, dimethylproflavine molecules stack on either side of the intercalated duplex, being related by a unit cell translation along b and a axes, respectively.

The basic structural feature of the sugar-phosphate chains accompanying dimethylproflavine intercalation in both structures is the mixed sugar puckering pattern: C3′ endo (3′-5′) C2′ endo. This same structural information is again demonstrated in the accompanying paper, which describes a complex containing dimethylproflavine with deoxyribo-CpG.

Similar information has already appeared for other “simple” intercalators such as ethidium, acridine orange, ellipticine, 9-aminoacridine, N-methyl-tetramethylphenanthrolinium and terpyridine platinum. “Complex” intercalators, however, such as proflavine and daunomycin, have given different structural information in model studies. We discuss the possible reasons for these differences in this paper and in the accompanying paper.     

Crystal and molecular structure of L-cis-3,6-dimethyl-2,5-piperazinedione (L-alanyl-L-alanyl-2,5-diketopiperazine)

The crystal structure of L -cis-3, 6-dimethyl-2,5-piperazinedione (L -alanyl-L -alanyl-2,5-diketopinerazine) has been determined. The unit cell is triclinic with a = 8.05, b = 6.08, c = 5.15 Å, α = 131.7°, β = 82.4°, γ = 106.6°. The space group is P1 with one molecule per unit cell. The six-membered ring is found to be nonplanar with an angle between the two amide group planes of 26°. One amide group deviates slightly from planarity. The experimental molecular model is discussed in terms of its flexibility.     

Copper(II) halide complexes of 2-aminobenzophenone. Crystal and molecular structure of bis(2-aminobenzophenone)dichlorocopper(II)

The complexes CuX₂L₂ (X = Cl, Br; L = 2-aminobenzophenone) were prepared and characterized by means of magnetic and spectroscopic measurements. For the Cl compound the crystal structure was also determined. Crystals are triclinic, space group P$\text{1}$, with a = 13.397(3), b = 10.752(2), c = 9.205(2) Å, α = 72.26(1)°, β = 91.58(1)°, γ = 106.86(1)°, and Z = 2. The structure was solved by the heavy-atom method and refined by least-squares calculations to R = 0.034 for 2581 counter data. It consists of discrete CuX₂L₂ monomers showing distorted trigonal bipyramidal coordination geometry about the copper ion. The amino nitrogens are axial ligands, with the equatorial positions occupied by two chlorine atoms and a carbonyl oxygen from one L molecule acting as a bidentate ligand. Infrared and ligand field spectroscopies and magnetic measurements, interpreted on the basis of the known crystal structure, also suggest a similar structure for the related Br compound.     

Chemical synthesis of polysaccharides. 7. Enzymatic hydrolysis of (1 → 6)-α-DL-glucopyranan (DL-dextran)

Hydrolysis of (1 → 6)-α-DL -glucopyranan (synthetic DL -dextran) by an endo-dextranase from a Penicillium species was examined in an acetate buffer solution (pH 5.3) at 37°C. Three samples of different tacticities (isotactic dyad content, 55, 63, and 72%) were employed with a clinical dextran for comparison. Colorimetric determination of the reducing end units of the saccharides produced during hydrolysis showed that the maximum degrees of hydrolysis based on the D-glucose units, (D.H.)_D, for the DL -dextrans were 21.4, 27.8, and 33.0% in the order of increasing isotacitic dyad content, whereas the (D.H.)_D value for the clinical dextran was 51.9%. A statistical treatment of the enzymatic hydrolysis is proposed to interpret the experimental results.     

Crystal structures of α- and β-(1,10-phenanthroline)tetrahydroborato(triphenylphosphine)copper(I) and (2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline)tetrahydroboratocopper(I)

Copper(I) is five coordinate in (1,10-phenanthroline)tetrahydroborato(triphenylphosphine)copper(I). This compound crystallizes from either toluene as the yellow, α-form, a = 16.247(8), b = 9.750(7), c = 9.322(5) Å, α = 62.92(4), β = 84.77(4), γ = 84.34(5)°, triclinic P$\text{1}$, Z = 2, or from a xylene/methylene chloride mixture as the red β-form, X-ray cell, a = 13.675(11), b = 10.115(8), c = 9.700(7) Å, α = 95.22(6), β = 96.22(6), γ = 101.02(6)°; neutron cell, as the tetradeuteroborate, a = 13.703(1), b = 10.096(8), c = 9.74(1) Å, α = 95.23(9), β = 96.51(8), γ = 101.04(2)°, triclinic, P$\text{1}$, Z = 2. For both forms, unidentate triphenylphosphine, bidentate 1,10-phenanthroline and unsymmetrical bidentate BH₄^? completes the copper(I) coordination but there are subtle differences between the two. When the ligand 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline, dmdp, replaces 1,10-phenanthroline, the compound obtained is four coordinate with no tpp in the crystal. [C(dmdp)BH₄] is monoclinic, Cc, a = 14.522(4), b = 20.07(2), c = 7.718(2) Å, β = 106.17(2)°, Z = 4.     

X-ray studies on crystalline complexes involving amino acids and peptides. Part XIV: Closed conformation and head-to-tail arrangement in a new crystal form of L-histidine L-aspartate monohydrate

A new form of L-histidine L-aspartate monohydrate crystallizes in space group P2₂ witha = 5.131(1),b = 6.881(1),c= 18.277(2) Å,β= 97.26(1)° and Z = 2. The structure has been solved by the direct methods and refined to anR value of 0.044 for 1377 observed reflections. Both the amino acid molecules in the complex assume the energetically least favourable allowed conformation with the side chains staggered between the α-amino and α-scarboxylate groups. This results in characteristic distortions in some bond angles. The unlike molecules aggregate into alternating double layers with water molecules sandwiched between the two layers in the aspartate double layer. The molecules in each layer are arranged in a head-to-tail fashion. The aggregation pattern in the complex is fundamentally similar to that in other binary complexes involving commonly occurring L amino acids, although the molecules aggregate into single layers in them. The distribution of crystallographic (and local) symmetry elements in the old form of the complex is very different from that in the new form. So is the conformation of half the histidine molecules. Yet, the basic features of molecular aggregation, particularly the nature and the orientation of head-to-tail sequences, remain the same in both the forms. This supports the thesis that the characteristic aggregation patterns observed in crystal structures represent an intrinsic property of amino acid aggregation.     

Crystallization of the purine salvage enzyme adenine phosphoribosyltransferase

Adenine phosphoribosyltransferase from the protozoan parasite Leishmania donovani has been crystallized in the presence of the substrate Mg²⁺-α-D -5-phosphoribosyl-1-pyrophosphate (PRPP) or the product adenosine-5-monophosphate, as well as in the absence of ligand. These crystals belong to the space group P6₁22 or its enantiomorph P6₅22, with unit cell dimensions of a = b = 64.0 Å, c = 240.5 Å, α = β = 90°, and γ = 120°. The crystals diffract to 1.9 Å. © 1996 Wiley-Liss, Inc.     

Crystal structure,conformational analysis,and molecular dynamics of tetra-O-methyl-(+) -catechin

The structure of tetra-O-methyl- (+) -catechin has been determined in the crystalline state. Two independent molecules, denoted structure A and structure B, exist in the unit cell. Crystals are triclinic, space group P1, a = 4.8125(2) Å, b = 12.9148(8) Å, c = 13.8862(11) Å, α = 86.962(6) °, β = 89.120(5)°, γ = 88.044(5)°, Z = 2, D_c = 1.336 g cm^?3, R = 0.033 for 6830 observations. The heterocyclic rings of the crystal structures are compared to previous results for 8-bromotetra-O-methyl-(+)-catechin, penta-O-acetyl-(+)-catechin, and (?) -epicatechin. One of the two molecules has a heterocyclic ring conformation similar to that observed previously for (?)-epicatechin, and the other has a heterocyclic ring conformation similar to one predicted earlier in a theoretical analysis of dimers of (+)-catechin and (?) -epicatechin. Both structure A and structure B in the crystal have heterocyclic ring conformations that place the dimethoxyphenyl substituent at C(2) in the equatorial position. However, this heterocyclic ring conformation does not explain the proton nmr coupling constant measured in solution. Molecular dynamics simulations show an equatorial ? axial interconversion of the heterocyclic ring, which can explain the nmr results. © 1993 John Wiley & Sons, Inc.     

Observation of a sterically unfavorable side-chain conformation in a leucyl residue: Crystal and molecular structure of L-leucyl–L-leucine · DMSO solvate

The crystal structure of a dipeptide L -leucyl–L -leucine (C₁₂H₂₄N₂O₃) has been determined. The crystals are monoclinic, space group P2₁, with a = 5.434(4) Å, b = 15.712(7) Å, c = 11.275(2) Å, β = 100.41(1)°, and Z = 2. The crystals contain one molecule of dimethyl sulfoxide (DMSO) as solvent of crystallization for each dipeptide molecule. The structure has been solved by direct methods and refined to a final R index of 0.059 for 920 reflections (sinθ/λ ? 0.60 Å^?1) with I ? 2σ (I). The trans peptide unit shows substantial degree of non-planarity (Δω = 14°). The peptide backbone adopts an extended conformation with torsion angles of ψ₁ = 138(1)°, ω₁ = 166(1)°, ?₂ = ? 149.3(7)°, ψ₂₁ = 164.2(7)°, and ψ₂₂ = ? 15(1)°. For the first leucyl residue, the side-chain conformation is specified by the torsion angles ¹χ₁ = 176.7(7)°, ¹χ₂₁ = 62(1)°, ¹χ₂₂ = ? 177.4(8)°; the second leucyl residue adopts a Sterically unfavorable conformation with ²χ₁ = 61(1)°, ²χ₂₁ = 97(1)°, and ²χ₂₂ = ?151(1)°. The packing involves head-to-tail interaction of peptide molecules and segregation of polar and nonpolar regions. The DMSO molecule is strongly hydrogen bonded to the terminal NH group. © 1994 John Wiley & Sons, Inc.     

Crystallization and preliminary X-ray crystallographic studies of nonhistone region of macroH2A.1

Histone macroH2A has a novel hybrid structure consisting of a large nonhistone region and a region that closely resembles a full-length histone H2A. One key to understanding macroH2A function is determining the structure and function of its nonhistone region. The nonhistone region of one of the two known macroH2A subtypes was expressed in Escherichia coli and purified using affinity and molecular sieve chromatography. Crystals of the protein suitable for structural studies were grown from polyethylene glycol solutions by vapor equilibration techniques. The crystals belong to the hexagonal space group P6₄ (or its enantiomorph P6₂) with unit cell parameters: a = b = 106.2 Å, c = 125.9 Å, α = β = 90°, and γ = 120°. There are four molecules in the asymmetric unit. Self-rotation function studies revealed three twofold noncrystallographic rotation axes related approximately by 222 symmetry. These crystals have 47% solvent content and diffract to 3.8 Å resolution. © 1995 Wiley-Liss, Inc.