Crystallographic study of plastocyanins

Crystals of plastocyanins from pea and corn leaves have been obtained. Both are suitable for X-ray structure analysis with a resolution up to 1.8 Å. The crystal form of plastocyanin from pea leaves belongs to the space group P2₁2₁2₁ with unit cell dimensions: $\text{a = 49.0}\text{A}\text{?}\text{, b = 53.3}\text{A}\text{?}\text{, c = 82.6}\text{A}\text{?}$. The assumed number of protein molecules per asymmetric unit of the unit cell is two. Crystals of the oxidized (Cu²⁺) and reduced (Cu⁺) forms are isomorphic. No essential differences in spot intensities for the main zone with a resolution of 3 Å were revealed. The crystal form of plastocyanin from corn leaves belongs to the space group P1 with unit cell parameters: $\text{a = 24.8}\text{A}\text{?}\text{, b = 30.0}\text{A}\text{?}\text{, c = 58.5}\text{A}\text{?}$ and α = 96° 10′, β = 87°08′, γ = 78°40′. The assumed number of protein molecules per asymmetric unit is two.     

Solution conformation and crystal structure of methyl 3,6-dideoxy-β-d-ribohexopyranoside,an immunodominant sugar of O-antigens

The crystal structure of methyl 3,6-dideoxy-β-d-ribohexopyranoside monohydrate was determined by direct methods. Crystals are monoclinic, space group P2₁, with cell dimensions $\text{a = 9.089(1), b = 7.668(1), c = 6.956(1)}\text{A}\text{?}\text{, β = 101.12°}$. The molecule adopts the ⁴C₁ chair conformation. The same conformation was also found in both aqueous and chloroform solutions. The pyranose ring is only slightly distorted, and the consequences of this observation on antigen structure are discussed.     

A preliminary crystallographic study of wheat germ agglutinin

Wheat germ agglutinin crystallizes in two monoclinic space groups, P2₁ and C2, under identical crystallization conditions. Unit cell dimensions are $\text{a = 73.8}\text{A}\text{?}\text{, b = 51.2}\text{A}\text{?}\text{, c = 90.8}\text{A}\text{?}\text{, γ = 90 °}$ for $\text{P2}{}_1\text{; a = 51.31}\text{A}\text{?}\text{, b = 73.35}\text{A}\text{?}\text{, c = 91.45}\text{A}\text{?}\text{, β = 97.75 °}$ for C2, both with eight subunit molecules in the unit cell. The C2 crystals were chosen as suitable for investigating the three-dimensional structure to high resolution, because of their smaller asymmetric unit (containing the dimer), and also because they display better diffraction patterns.     

Visualization of drug-nucleic acid interactions at atomic resolution: II. Structure of an ethidium/dinucleoside monophosphate crystalline complex,ethidium:5-iodocytidylyl (3′–5′) guanosine

Ethidium forms a second crystalline complex with the dinucleoside monophosphate 5-iodocytidylyl(3′–5′)guanosine (iodoCpG). These crystals are monoclinic, P2₁, with $\text{a = 14.06}\text{A}\text{?}\text{, b = 32.34}\text{A}\text{?}\text{, c = 16.53}\text{A}\text{?}\text{, β = 117.8 °}$. The structure has been solved to atomic resolution using rigid-body Patterson vector search and Fourier methods, and refined by full matrix least-squares to a residual of 0.16 on 3180 observed reflections. The structure consists of two ethidium molecules, two iodoCpG molecules, 27 water molecules and four methanol molecules, a total of 165 atoms (excluding hydrogens) in the asymmetric unit. Both iodoCpG molecules are hydrogen-bonded together by guanine · cytosine Watson-Crick base-pairing. Adjacent base-pairs within this paired iodoCpG structure and between neighboring iodoCpG molecules in adjoining unit cells are separated by 6.7 Å. This distance reflects the presence of an ethidium molecule intercalated between base-paired iodoCpG molecules and another ethidium molecule stacked above (and below) the dinucleotide. Approximate 2-fold symmetry is used in the interaction; this reflects the pseudo-2-fold symmetry axis of the phenanthridinium ring system in ethidium coinciding with the approximate 2-fold axis relating base-paired iodoCpG molecules. The phenyl and ethyl groups of the intercalated ethidium molecule lie in the narrow groove of the miniature iodoCpG double-helix. The stacked ethidium, however, lies in the opposite direction, its phenyl and ethyl groups neighboring iodine atoms on cytosine residues. Base-pairs within the paired nucleotide units are related by a twist of about 8 °. The magnitude of this angular twist reflects conformational changes in the sugar-phosphate chains accompanying intercalation. These primarily reflect the differences in ribose sugar ring puckering that are observed (i.e. both iodocytidine residues have C3′ endo sugar conformations, while both guanosine residues have C2′ endo sugar conformations), and alterations in the glycosidic torsional angles that describe the base-sugar orientation.The information provided by this structure analysis (along with the accompanying one (ethidium:iodoUpA), described in the previous paper) has led to an understanding of the general nature of intercalative drug binding to DNA. This is described in the third paper of this series.     

Structural investigations of mode of action of drugs. I. Molecular structure of mitomycin C.

The crystal and molecular structure of the antitumor antibiotic mitomycin C has been determined by X-ray diffraction. The space group is monoclinic P2₁ with cell dimensions $\text{a}\text{=77.988(3)}$, $\text{b}\text{=20.355(7)}$, $\text{c}\text{=9.679(3)}\text{A}\text{?}$, β=95.99°(1) and Z=4. The structure was solved by direct methods. There are two independent molecules per asymmetric unit. The structure was refined to an R value of 0.049 for 2151 observed reflections measured on diffractometer. The benzoquinone ring is slightly deviated from planarity. The N4 in the indole ring behaves like an amide nitrogen owing to its participation in the conjugated benzoquinoid system. The five membered ring through C1, C2, C3, N4 and C9a adopts an envelope conformation. The molecules are held together in crystal by the hydrogen bonds. All nitrogens except N4 are involved in the hydrogen bonding. Studies with models of drug and DNA indicate two different kinds of mechanism for crosslinking.     

Preliminary X-ray data for the ribose binding protein from Salmonella typhimurium

Crystals of the periplasmic ribose binding protein of Salmonella typhimurium have been subjected to X-ray analysis. The crystals grow as rectangular parallelopipeds with the symmetry of space group P2₁. Unit cell dimensions are $\text{a = 64·4}\text{A}\text{?}\text{, b = 60·6}\text{A}\text{?}\text{, c = 62·8}\text{A}\text{?}$, and β = 91·25 °. There are two molecules of molecular weight 29,000 per asymmetric unit.     

Highly ordered crystals of the plant seed protein crambin.

Crystals of crambin, a plant seed protein of molecular weight 5000, diffract X-rays strongly to the interplanar spacing limit of 0.88 Å. These diffraction data should allow a definition of atomic structure that is on a par with that typically obtained from crystals of small organic molecules. The crystals are in space group P2₁ and have unit cell dimensions $\text{a = 41.1}\text{A}\text{?}\text{, b = 18.7}\text{A}\text{?}\text{, c = 22·7}\text{A}\text{?}\text{,}\text{and}\text{β = 90.6 °}$. The asymmetric unit contains one protein molecule.     

A preliminary crystallographic investigation of rabbit muscle creatine kinase

Three crystal forms of rabbit muscle creatine kinase have been grown, one of which seems suited to a high resolution X-ray diffraction study. The first form is of monoclinic space group P2₁ with $\text{a = 54}\text{A}\text{?}\text{, b = 114}\text{A}\text{?}\text{, c = 145}\text{A}\text{?}\text{, β = 91 °}$ and has as the asymmetric unit two molecules of total molecular weight 160, 000. The second form, grown in the presence of mercurials, is of space group A2 with $\text{a = 52}\text{A}\text{?}\text{, b = 165}\text{A}\text{?}\text{, c = 237}\text{A}\text{?}\text{, β = 91 °}$ and also has two molecules in the asymmetric unit. The third crystal form, grown in the presence of a high concentration of cysteine, is of apparent space group P2₁2₁2₁, but evidence indicates that the true space group may be P2₁22₁. The dimensions of the orthorhombic unit cell are $\text{a = 47}\text{A}\text{?}\text{, b = 86}\text{A}\text{?}\text{, c = 125}\text{A}\text{?}$, and the asymmetric unit contains a single protein subunit. Assuming the latter space group, then the creatine kinase molecule possesses a twofold axis relating two identical subunits.     

Crystallization of ribonuclease St

The crystals of ribonuclease St, the extracellular ribonuclease from Streptomyces erythreus, have been obtained from (NH₄)₂SO₄ solution with acetate buffer (pH 4.1). The crystals belong to a monoclinic space group C2 with dimensions $\text{a = 88.4}\text{A}\text{?}\text{, b = 33.0}\text{A}\text{?}\text{, c = 69.0}\text{A}\text{?}\text{, β = 98.4 °}$. There are two protein molecules per asymmetric unit. The crystals diffract beyond 2.0 Å resolution.     

Polar group interaction and molecular packing of membrane lipids: The crystal structure of lysophosphatidylethanolamine

The conformation and molecular packing of 3-palmitoyl-dl-glycerol-1-phosphoryl-ethanolamine has been determined by a single crystal analysis (R = 0.115); it crystallizes in the monoclinic space group $\text{P2}{}_1\text{a}$ with a unit cell of $\text{a = 7.66}\text{A}\text{?}\text{, b = 9.08}\text{A}\text{?}\text{, c = 37.08}\text{A}\text{?}\text{and}\text{β = 90.2 °}$, with four molecules per unit cell. The molecules exist as configurational and conformational enantiomers and pack in a bilayer arrangement. The phosphorylethanolamine groups have an orientation parallel to the layer surface. The hydrocarbon chains are arranged according to the T∥ chain packing mode and adopt an extreme tilt of 57.5 ° with respect to the layer normal. The free glycerol hydroxyl group forms an intramolecular hydrogen bond with, a phosphate oxygen and thus affects the conformation and orientation of the head group. The phosphorylethanolamine dipoles are oriented parallel to each other in double rows, while they are antiparallel and form a continuous network in dilauroylphosphatidylethanolamine (Elder et al., 1977). The area per molecule in 3-palmitoyl-dl-glycerol-1-phosphorylethanolamine (34.8 Ų) is less than in diacylphosphatidylethanolamine (38.6 Ų), indicating that in the latter the hydrocarbon chains determine the molecular cross-section. The significance of the interaction and space requirement of the phosphorylethanolamine group for the phase behaviour of phosphatidylethanolamine is discussed.     

Disco-ordinate expression of the Escherichia coli gal operon after prophage lambda induction.

EcoRI endonuclease crystallizes in space group C2 with unit cell parameters $\text{a = 209}\text{A}\text{?}\text{, b = 129}\text{A}\text{?}\text{, c = 50}\text{A}\text{?}\text{and}\text{β = 98.4 °}$. Four 29,000 molecular weight subunits per asymmetric unit would give a reasonable V_m value of 2.87 ų/dalton. EcoRI endonuclease is the first protein which recognizes a specific sequence of bases in DNA to be crystallized in a form suitable for high resolution structure analysis.     

Crystallographic data for lysozyme from the egg white of the Embden goose

Two crystal forms of lysozyme from the egg white of the embden goose (Anser anser) have been obtained, both of which are suitable for X-ray diffraction analysis. The monoclinic form has space group P2₁ with cell dimensions $\text{a = 38.3}\text{A}\text{?}\text{, b = 65.7}\text{A}\text{?}\text{, c = 45.2}\text{a}\text{?}$, β = 116 ° and the triclinic form (space group P1) has cell dimensions of $\text{a = 39.9}\text{A}\text{?}\text{, b = 42.2}\text{A}\text{?}\text{, c = 57.9}\text{A}\text{?}$ and α = 98.8 °, β = 102.5 °, γ = 90.5 °.     

Crystallization of mouse submaxillary gland renin

Renin isolated from the mouse submaxillary gland has been crystallized and is being subjected to X-ray diffraction analysis.The observed crystalline form has the following unit cell dimensions: $\text{a = 96.4 (1)}\text{A}\text{?}\text{, b = 104.4 (1)}\text{A}\text{?}\text{, c = 77.4 (1)}\text{A}\text{?}\text{, β = 101.2 (1) °}$, space group P2₁, Z = 8 (4 protein molecules in the asymmetric unit).Native data have been recorded at 5 Å resolution with an automatic diffractometer.     

Preliminary crystallographic data for exfoliative toxin B from Staphylococcus aureus

The serotype B of exfoliative toxin, isolated from Staphylococcus aureus, strain TC 142, has been crystallized. The monoclinic crystals belong to space group P2₁, with $\text{a = 55.9}\text{A}\text{?}\text{, b = 107.9}\text{A}\text{?}\text{, c = 42.8}\text{A}\text{?}\text{, and}\text{β = 90.9 °}$. The asymmetric unit contains two molecules of molecular weight 30,000.     

X-ray study on egg-yolk lecithin: Unit cell data and electron density profile

The unit cell dimensions and space group of egg-yolk lecithin (l-α-phosphatidylcholine) in the crystalline state were obtained from a set of X-ray fibre diagrams recorded from specimens oriented in two different axes; $\text{a = 8.84}\text{A}\text{?}\text{± 0.05}\text{A}\text{?}\text{, b = 10.07}\text{A}\text{?}\text{± 0.05}\text{A}\text{?}\text{, c = 54.69}\text{A}\text{?}\text{± 0.05}\text{A}\text{?}$, with space group P2₁2₁2, and four molecules per unit cell. From the 00l reflexions up to the 25th order, an electron density profile is obtained which is consistent with a probable structure of the molecule.     

Glycerol conformation and molecular packing of membrane lipids: The crystal structure of 2,3-dilauroyl-d-glycerol

The single-crystal structure of 2,3-dilauroyl-d-glycerol has been determined by Patterson rotation and translation methods and refined to R = 0.069. 2,3-dilauroyl-d-glycerol crystallizes in the monoclinic space group P2₁, with unit cell dimensions: $\text{a = 5.46}\text{A}\text{?}\text{, b = 7.59}\text{A}\text{?}\text{, c = 34.2}\text{A}\text{?}\text{and}\text{β = 93.1 °}$, and with two molecules per unit cell. The molecules have their hydrocarbon chains aligned parallel, and are arranged in a bilayer structure. The chain stacking is achieved by a bend in the fatty acid. The hydrocarbon chains pack according to the orthorhombic perpendicular chain packing mode, and are tilted 26.5 ° from the layer normal.The structural features of 2,3-dilauroyl-d-glycerol have been analysed with reference to the corresponding hydrophobic moieties in the crystal structures of different membrane lipids. The glycerol group in 2,3-dilauroyl-d-glycerol is oriented parallel to the layer plane, but changes to an approximately layer-perpendicular orientation when a polar group is attached. The molecular conformation of the glycerol-dicarboxylic ester group, however, is identical in both the absence and presence of a head group, indicating extensive conformational restrictions for this group due to both intrinsic properties and chain stacking. The gathered data provide detailed information on the structural properties of the hydrophobic moiety of membrane lipids.     

Characterization of a monoclinic crystal form of an enzyme of steroid metabolism, Δ5-3-ketosteroid isomerase

A monoclinic crystal form ($\text{P2}{}_1\text{, a = 140.4}\text{A}\text{?}\text{, b = 85.0}\text{A}\text{?}\text{, c = 94.5}\text{A}\text{?}$, β= 130.1 °) of Δ⁵-3-ketosteroid isomerase from Pseudomonas testosteroni (EC 5.3.3.1), grown at pH 7.0, has been characterized. Crystal-density measurements show that the asymmetric unit contains 12 protomers (M_r = 13,394).     

Crystallographic data for a penicillin receptor : exocellular DD-carboxypeptidase-transpeptidase from Streptomyces R61.

A pencillin-sensitive enzyme, the exocellular dd-carboxypeptidase-transpeptidase from Streptomyces R61, has been crystallized from polyethylene glycol (M_r = 6000 to 7500) solution at pH 7·6. X-ray examination of the orthorhombic crystals shows the space group is P2₁2₁2₁, with unit cell dimensions $\text{a = 51·1}\text{A}\text{?}\text{, b = 67·4}\text{A}\text{?}\text{,}\text{and}\text{c = 102·9}\text{A}\text{?}$. With four molecules of molecular weight 38,000, the $\text{A}\text{?}{}^3\text{/}\text{dalton}$ ratio for the cell is 2·33. The crystals are stable to irradiation for 75 hours and are suitable for structure analysis to at least 2·4 Å resolution. The radius of gyration of the molecule in solution at pH 6.8 is 20.8 Å.     

X-ray diffraction analysis of crystals of bovine platelet factor 4

Bovine platelet factor 4 has been crystallized by “vapor dilution” in space group P2₁2₁2₁, $\text{a = 63.7}\text{A}\text{?}\text{, b = 66.7}\text{A}\text{?}\text{, c = 80.5}\text{A}\text{?}$, with four molecules, each 9505 M_r, in the asymmetric unit. The crystals diffract X-rays to better than 2.8 Å resolution.     

Crystallographic study of the iron-sulfur flavoprotein trimethylamine dehydrogenase from the bacterium W3A1

Large single crystals of trimethylamine dehydrogenase, containing both [4Fe-4S]²⁺ centers and covalently bound FMN, have been prepared by the macro seeding technique. The crystals are monoclinic, space group P2₁ with cell parameters $\text{a = 147.63}\text{A}\text{?}\text{, b = 71.96}\text{A}\text{?}\text{, c = 83.66}\text{A}\text{?}\text{and}\text{β = 97.64 °}$, and diffract to at least 2.0 Å resolution. There is one dimer of approximately 166,000 M_m per asymmetric unit. A 5.0 Å resolution anomalous scattering difference Patterson has been computed which shows the presence and position of two [4Fe-4S]²⁺ centers in the asymmetric unit. A self-rotation function computed at 6.0 Å resolution indicates a non-crystallographic 2-fold axis relating the two subunits. These results show trimethylamine dehydrogenase to be composed of two identical or very similar subunits each containing one [4Fe-4S]²⁺ center.