Crystallization and preliminary X-ray crystallographic studies of L-2-haloacid dehalogenase from Pseudomonas sp. YL

The dimeric L -2-haloacid dehalogenase from Pseudomonas sp. YL, (subunit mass, 26179 Da), has been crystallized by vapor diffusion, supplemented by repetitive seeding, against a 50 mM potassium dihydrogenphosphate solution (pH 4.5) containing 15% (w/v) polyethylene glycol 8,000 and 1% (v/v) n-propanol. The crystals belong to the monoclinic space group C2 with unit cell dimensions of a = 92.21 Å, b = 62.78 Angst; c = 50.84 Å, and β = 122.4°, and contain two dehalogenase dimers in the unit cell. They are of good quality and diffract up to 1.5 Å resolution.     

Crystallization and preliminary crystallographic analysis of the N-terminal two domain fragment of vascular cell adhesion molecule-1 (VCAM-1)

A molecular fragment comprising the first two domains of the human vascular cell adhesion molecule-l (VCAM-l) has been crystallized by the vapor diffusion method. Two crystal forms have been examined by X-ray analysis: One crystal form belongs to the space group C2 with two molecules in the asymmetric unit and cell parameters: a = 122.1 Å, b = 48.9 Å, c = 73.4 Å, and β = 117.4°. The other crystal form belongs to the space group P2₁ with one molecule in the asymmetric unit and cell parameters: a = 40.4 Å, b = 45.7 Å, c = 54.7 Å, and β = 100.5°. Diffraction data up to 1.9 Å resolution have been collected for the C2 crystal form. © 1994 Wiley-Liss, Inc.     

Channel‐like crystal structure of cinchoninium L‐O‐phosphoserine salt dihydrate

Studies on the interactions between L ‐O‐ phosphoserine, as one of the simplest fragments of membrane components, and the Cinchona alkaloid cinchonine, in the crystalline state were performed. Cinchoninium L ‐O‐phosposerine salt dihydrate (PhSerCin) crystallizes in a monoclinic crystal system, space group P2₁, with unit cell parameters: a = 8.45400(10) Å, b = 7.17100(10) Å, c = 20.7760(4) Å, α = 90°, β = 98.7830(10)°, γ = 90°, Z = 2. The asymmetric unit consists of the cinchoninium cation linked by hydrogen bonds to a phosphoserine anion and two water molecules. Intermolecular hydrogen bonds connecting phosphoserine anions via water molecules form chains extended along the b axis. Two such chains symmetrically related by twofold screw axis create a “channel.” On both sides of this channel cinchonine cations are attached by hydrogen bonds in which the atoms N1, O12, and water molecules participate. This arrangement mimics the system of bilayer biological membrane. Chirality 2010. © 2009 Wiley‐Liss, Inc.     

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.     

Crystallization and preliminary x-ray diffraction studies of a monoclonal antibody fab fragment against foot-and-mouth disease virus and of its complex with the main antigenic site peptide

The Fab fragment of the neutralizing monoclonal antibody SD6 elicited against foot-and-mouth disease virus (FMDV) C-SBcl and its complex with a peptide, corresponding to the major antigenic site of FMDV (VPl residues 136–150, YTASARGDLAHLTTT), have been crystallized using the hanging drop vapor diffusion techniques. For the isolated Fab, crystals diffracting to 2.5 Å resolution were obtained at room temperature using ammonium sulfate as precipitant. These crystals are monoclinic, space group C2, and unit cell parameters a = 109.53 Å, b = 89.12 Å, c = 64.04 Å, and β = 112.9° and contain one Fab molecule per asymmetric unit. Crystals from the complex diffract, at least, to 2.8 Å resolution and were obtained, at room temperature, using PEG as precipitant. These crystals are monoclinic, space group P2, and unit cell parameters a = 56.11 Å, b = 60.67 Å, c = 143.45 Å, and β = 95.4°, Density packing considerations indicate that there are two Fab molecules in the asymmetric unit. © 1994 John Wiley & Sons, Inc.     

Conformational studies of peptides: Crystal and molecular structures of L-3,4-dehydroproline and its t-butoxycarbonyl and acetyl amide derivatives

The crystal structures of L -3,4-dehydroproline, t-butoxycarbonyl-L -3,4-dehydroproline amide, and acetyl-L -3,4-dehydroproline amide have been determined. L -3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L -3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L -3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L -3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L -3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L -3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L -3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present ? and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have ? and ψ values corresponding to a collagenlike conformation (conformation F).     

Growth and analysis of crystal forms of toxic shock syndrome toxin 1

Native toxic shock syndrom toxin 1 (TSST-1) purified from Staphylococcus aurius has been crystallized in four different forms. The highest resolution data (2.05 Å) was collected from orthorhombic crystals belonging to the space group C222₁. The unit cell dimension are a = 108.7 Å, b = 177.5 Å, c = 97.6 Å. Rotation function analysis of this from indicates that there is trimer of toxin molecules in the asymmetric unit with a local 3-fold axis parallel to the crystallographic c axis. Crystals of a double mutant of TSST-1 have been grown which has a single molecule in the asymmetric unit and diffract to 1.9 Å. The space group is P2₁ with unit cell parameters of a = 44.4 Å, b = 34.0 Å, c = 55.2 Å, β = 93.0°. © 1993 Wiley-Liss, Inc.     

Conformational variability of Gly-Gly segments in peptides: A comparison of the crystal structures of an acyclic pentapeptide and an octapeptide

The crystal structure of an acyclic pentapeptide, Boc-Gly-Gly-Leu-Aib-Val-OMe, reveals an extended conformation for the Gly-Gly segment, in contrast to the helical conformation determined earlier in the octapeptide Boc-Leu-Aib-Val-Gly-Gly-Leu-Aib-Val-OMe [I. L. Karle, A. Banerjee, S. Bhattacharjya, and P. Balaram [1996] Biopolymers, Vol. 38, pp. 515–526). The pentapeptide crystallizes in space group P2₁ with one molecule in the asymmetric unit. The cell parameters are: a = 10.979(2) Å, b = 9.625(2) Å, c = 14.141(2) Å, and β = 96.93(1)°, R = 6.7% for 2501 reflections (I > 3σ(I)). The Gly-Gly segment is extended (ϕ₁ = −92°, ψ₁ = −133°, ϕ₂ = 140°, ψ₂ = 170°), while the Leu-Aib segment adopts a type II β-turn conformation (ϕ₃ = −61°, ψ₃ = 130°, ϕ₄ = 71°, ψ₄ = 6°). The observed conformation for the pentapeptide permits rationalization of a structural transition observed for the octapeptide in solution. An analysis of Gly-Gly segments in peptide crystal structures shows a preference for either β-turn or extended conformations. © 1997 John Wiley & Sons, Inc.     

Crystallization and preliminary X-ray diffraction study of the green flavoenzyme 5-Hydroxyvaleryl-CoA dehydratase/dehydrogenase from Clostridium aminovalericum

The bifunctional flavoenzyme 5-hydroxyvaleryl-CoA dehydratase/ dehydrogenase has been crystallized from solutions containing ammonium sulfate (form I) or polyethylene glycol (form II) as precipitant. In both cases, the crystals grew in the monoclinic space group C2. The unit cell dimensions for form I crystals were determined as a = 162.8 Å, b = 71.8 Å, c = 83.5 Å, β = 109.1°. Corresponding values for form II crystals were a = 161.2 Å, b = 71.6 Å, c = 82.2 Å, β = 109.3°. In both cases most probably there are two monomers per asymmetric unit. The crystals diffract to about 2 Å resolution and are rather stable in the X-ray beam. © 1994 Wiley-Liss, Inc.     

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.     

Crystal structure of dehydromonopetide, (Z)-N-acetyl-α,β-dehydrophenylalanine methylamide

The crystal structure of (Z)-acetyl-α,β-dehydrophenylalanine methylamide (monoclinic Cc, a = 10.241(1), b = 15.252(1), c = 8.643(1) Å, β = 120.98(1)°, Z = 4) has been solved by x-ray diffraction to an R-factor = 0.148, and compared to that of the homologous L -phenylalanine dervative. Molecules are intermolecularly hydrogen-bonded to four neighboring molecules in a three-dimensional network with alternating layers of interacting amide bonds and orthogonally arranged phenyl rings. The existence of the C^α = C^β double bond results in a phenyl orientation that is forbidden for phenylananine (χ¹ = ?7,8°), and in shorter C^α ? C^β and C^β ? C^γ distances. The geometrical paramenters of the peptide backbone are not drastically modified by α,β-unsaturation. However, the N-C^α-C′ angle is increased by nearly 5°, and the dimensions, and therefore probably the electronic conjugation, of the N-terminal amide group to be affected by the occurrence of the vicinal C^α = C^β double bond.     

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.     

Crystallization and preliminary X-ray diffraction studies of formylmethanofuran: Tetrahydromethanopterin formyltransferase from Methanopyrus kandleri

Formylmethanofuran:tetrahydromethanopterin formyltransferase from the hyperthermophilic methanogenic Archaeon Methanopyrus kandleri (growth temperature optimum 98°C) was crystallized by vapor diffusion methods. Crystal form M obtained with 2-methyl-2,4-pentanediol as precipitant displayed the space group P2₁ with unit cell parameters of a = 87.0 Å, b = 75.4 Å, c = 104.7 Å, and β = 113.9° and diffracted better than 2 Å resolution. Crystal form P grown from polyethylene glycol 8000 belonged to the space group I4₁22 and had unit cell parameters of 157.5 Å and 242.1 Å. Diffraction data to 1.73 Å were recorded. Crystal form S which was crystallized from (NH₄)₂SO₄in the space group I4₁22 with unit cell parameters of 151.3 Å and 249.5 Å diffracted at least to 2.2 Å resolution. All crystal forms probably have four molecules per asymmetric unit and are suitable for X-ray structure analysis. © 1996 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.     

Crystallization and preliminary X-ray analysis of volvatoxin A2 from Volvariella volvacea

Volvatoxin A2, an ion channel disturbed cardiotoxic and hemolytic protein from the edible mushroom, Volvarilla volvacea, has been crystallized by the vapor diffusion method using polyethylene glycol 4000 and ammonium sulfate in sodium acetate buffer pH 4.6. The best crystals belong to the monoclinic space group C2 with unit cell dimensions a = 155.25 Å, b = 58.06 Å, c = 116.92 Å, and β = 119.5°. These crystals diffract to at least 2.2 Å and there are four molecules of molecular weight 24 kDa per asymmetric unit with a solvent content of 48%.     

Crystallization and preliminary X-ray diffraction studies of leishmanolysin,the major surface metalloproteinase from Leishmania major

The membrane-bound GPI-anchored zinc metalloproteinase leishmanolysin purified from Leishmania major promastigotes has been crystallized in its mature form. Two crystal forms of leishmanolysin have been grown by the vapor diffusion method using 2-methyl-2,4-pentanediol as the precipitant. Macroseeding techniques were employed to produce large single crystals. Protein microhet-erogeneity in molecular size and charge was incorporated into both crystal forms. The tetragonal crystal form belongs to the space group P4₁2₁2 or the enantiomorph P4₃2₁2, has unit cell parameters of a = b = 63.6 Å, c = 251.4 Å, and contains one molecule per asymmetric unit. The second crystal form is monoclinic, space group C2, with unit cell dimensions a = 107.2 Å, b = 90.6 Å, c = 70.6 Å, β = 110.6°, and also contains one molecule per asymmetric unit. Both crystal forms diffract X-rays beyond 2.6 Å resolution and are suitable for X-ray analysis. Native diffraction data sets have been collected and the structure determination of leishmanolysin using a combination of the isomorphous replacement and the molecular replacement methods is in progress. © 1995 Wiley-Liss, Inc.     

Electron diffraction of Valonia cellulose. A quantitative interpretation

The crystal structure of native cellulose (Valonia) has been analyzed by electron diffraction. Possible models for the structure were refined by rigid-body least squares methods, which incorporated parameters defining the preferred orientation of the fibrils around their long axes in the cell wall lamellae. The structure was found to consist of an array of chains having the same sense (i.e., parallel), with packing parameters similar to those recently determined by X-ray diffraction. The eight-chain unit cell could be approximated adequately by a two-chain monoclinic unit cell with dimensions a = 8.18 Å, b = 7.84 Å, c = 10.38 Å (fiber axis), and γ = 97.04°; the space group is P2₁.     

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.     

Purification,crystallization, and preliminary X-ray diffraction analyses of the bacterial chemotaxis receptor modifying enzymes

Bacterial chemotaxis receptor modifying enzymes from Salmonella typhimurium have been crystallized using microseeding techniques. The crystals of the S-adenosyl-L -methionine-dependent methyl transferase, CheR, belong to the monoclinic space group P2₁ with cell constants a = 55.1 Å, b = 48.1 Å, c = 63.1 Å, β = 112.3°. The crystals of the catalytic domain of the methylesterase, CheB, belong to the trigonal space group P3₂21 or P3₁21 with unit cell dimensions of a = b = 63.4 Å, c = 86.8 Å. Both crystals contain one molecule per asymmetric unit and have calculated Matthews' volumes of 2.4 ų/Da. © 1995 Wiley-Liss, Inc.