Molecules In Asymmetric Unit Research Articles

On the presence of multiple molecules in the crystal asymmetric unit (Z′ > 1)

On the presence of multiple molecules in the crystal asymmetric unit (Z′ > 1)

Comment on “On the presence of multiple molecules in the crystal asymmetric unit (Z′ > 1)” by Gautam R. Desiraju, CrystEngComm, 2007,9, 91

A reply to the Desiraju letter concerning multiple molecules in the asymmetric unit.

Structural Studies of the Polymorphs of Carbamazepine, Its Dihydrate, and Two Solvates

High-field cross-polarisation magic-angle spinning 13C NMR spectra are presented for the four known polymorphs of anhydrous carbamazepine, for a dihydrate, and for two solvates. These are all distinctive, despite relatively low spectral dispersion, and give immediate information about the crystallographic asymmetric unit. The results for the trigonal and the two monoclinic forms are consistent with the published crystal structures. That of the triclinic form was found to contain four molecules in the crystallographic asymmetric unit, which has recently been confirmed by an X-ray diffraction study. NMR shows that the dihydrate has one molecule in the asymmetric unit, and the full crystal structure derived from single-crystal X-ray diffraction work is reported herein. It is found to be ordered and monoclinic, in contrast to the reported disordered orthorhombic structure. The discrepancy is attributed to the common occurrence of multiple micro-twinning. Shielding computations using a method which takes explicit account of the repetition inherent in a crystal lattice are reported for the P-monoclinic form and are compared to the experimental chemical shifts. The NMR data of all the forms are discussed in relation to variations in the molecular geometry of the hydrogen-bonded dimers (except in the case of two solvates). Chemical shift variations are explored as a function of the amide torsion using the Gaussian computer program.

Crystal Structure of Vinorine Synthase, the First Representative of the BAHD Superfamily

Vinorine synthase is an acetyltransferase that occupies a central role in the biosynthesis of the antiarrhythmic monoterpenoid indole alkaloid ajmaline in the plant Rauvolfia. Vinorine synthase belongs to the benzylalcohol acetyl-, anthocyanin-O-hydroxy-cinnamoyl-, anthranilate-N-hydroxy-cinnamoyl/benzoyl-, deacetylvindoline acetyltransferase (BAHD) enzyme superfamily, members of which are involved in the biosynthesis of several important drugs, such as morphine, Taxol, or vindoline, a precursor of the anti-cancer drugs vincaleucoblastine and vincristine. The x-ray structure of vinorine synthase is described at 2.6-angstrom resolution. Despite low sequence identity, the two-domain structure of vinorine synthase shows surprising similarity with structures of several CoA-dependent acyltransferases such as dihydrolipoyl transacetylase, polyketide-associated protein A5, and carnitine acetyltransferase. All conserved residues typical for the BAHD family are found in domain 1. His160 of the HXXXD motif functions as a general base during catalysis. It is located in the center of the reaction channel at the interface of both domains and is accessible from both sides. The channel runs through the entire molecule, allowing the substrate and co-substrate to bind independently. Asp164 points away from the catalytic site and seems to be of structural rather than catalytic importance. Surprisingly, the DFGWG motif, which is indispensable for the catalyzed reaction and unique to the BAHD family, is located far away from the active site and seems to play only a structural role. Vinorine synthase represents the first solved protein structure of the BAHD superfamily.

Morphology, Crystal Structure, and Thermal and Spectral Studies of Semiorganic Nonlinear Optical Crystal LAHClBr

Solubility and specific heat properties of the semiorganic nonlinear optical crystal, L-arginine hydrocholorobromide (LAHClBr), have been measured as a function of temperature. The compound crystallizes in a rectangular bipyramidal shape with well-developed {100} and {001} pinacoids. X-ray diffraction analysis shows that it belongs to the space group P2 1 with two independent molecules in asymmetric units and lattice parameters a = 11.158(2) A, b = 8.579(3) A, c = 11.235(3) A, β = 91.55°(4). The arginine molecules occur as zwitterions, with the amino groups and the guanidyl groups each accepting a proton from the acid groups present in the molecule. The molecules are held together by a three-dimensional network of hydrogen bonds.

Few molecules in asymmetric unit; why?

Few molecules in asymmetric unit; why?

Approaches to very low resolution phasing of the ribosome 50S particle from Thermus thermophilus by the few-atoms-models and molecular-replacement methods.

Estimates for the phases of the X-ray diffraction data from the 50S ribosomal particle of Thermus thermophilus has been made to an effective resolution around 80 A using the few-atoms-modes ab initio technique [Lunin, Lunina, Petrova, Vernoslova, Urzhumtsev & Podjarny (1995). Acta Cryst. D51, 896-903]. This technique models the density with a small number of Gaussian spheres to generate a large number of possible phase sets and then uses clustering algorithms to identify the best ones. Independently, an envelope obtained from electron-micrograph image reconstruction [Yonath, Leonard & Wittmann (1987). Science, 236, 813-816] was oriented and positioned using the molecular-replacement technique, specially adapted to the very low resolution case [Urzhumtsev & Podjarny (1995). Acta Cryst. D51, 888-895]. The two methods show similar packing arrangements. The electron density calculated by the few-atoms-models technique without any assumption on the number of molecules in asymmetric unit or on their shape shows recognizable features of the particle.

Polypurine tract DNA sequence, CAAAGAAAAG containing 2 molecules in asymmetric unit. Is the 2nd helix disordered?

Polypurine tract DNA sequence, CAAAGAAAAG containing 2 molecules in asymmetric unit. Is the 2nd helix disordered?

Structure of a functional fragment of VCAM-1 refined at 1.9 a resolution.

The crystal structure of the functional amino-terminal two-domain fragment of human vascular cell adhesion molecule 1 (VCAM-1) has been determined at 1.9 A resolution. The crystals contain two copies of the molecule in the asymmetric unit. The structure was solved by multiple isomorphous replacement, using lead and selenium derivatives. Anomalous scattering had to be used to resolve the phase ambiguity of a lead derivative. Since the selenium derivative has very small isomorphous differences, the local scaling algorithm had to be used to obtain an interpretable difference Patterson map. The initial phases were improved by non-crystallographic averaging, solvent flattening and histogram matching. The structure has been refined to a crystallographic R factor of 20.4% (15-1.9 A, F>/= 3sigma) and consists of two Ig domains (D1 and D2). The angle between these domains differs by 12 degrees between the two copies of the molecule in the crystallographic asymmetric unit, demonstrating that some movement is possible at the interface. In the amino-terminal domain D1 there is an 'extra' disulfide bond, in addition to the conserved cross-sheet disulfide bond, at the top of the molecule. This bond, a hallmark of the integrin-binding subclass of Ig superfamily proteins, makes the top of this domain very compact. The feature that projects most prominently from D1 is the CD loop, near the base of the domain. The key residue for integrin binding, Asp40, is located in this loop and is easily accessible.

Refined Crystal Structure of Rat Parvalbumin, a Mammalian α-lineage Parvalbumin, at 2·0 Å Resolution

We present here the X-ray crystal structure of the rat α-parvalbumin from fast twitch muscle. This protein ( M r 11·8kDa) crystallizes in space group P2 12 12 1 with unit cell dimensions of a=34·3 Å, b=55·0 Å, c=156·1 Å and three molecules in the asymmetric unit. The protein structure was solved by the molecular replacement method and has been refined to a crystallographic R-factor ( R=Σ∥ F o|-| F c∥/Σ| F o|)) of 0·181 for all reflections with I/σ(I)(l) ≥ 2 ( I=intensity) between 8·0 and 2·0 Å resolution. The molecules located most easily in the molecular replacement rotation function had lower overall thermal motion parameters and higher numbers of intermolecular crystal packing contacts. The overall fold of the polypeptide chain for the rat α-parvalbumin is similar to other known parvalbumin structures (root-mean-square deviations in α-carbon atom positions range from 0·60 to 0·87 Å). There are two Ca 2+-binding sites in parvalbumins, and them is some evidence for a third ion-binding site, adjacent to the CD site, in the rat species. The level of structural variability among the best-ordered regions of the three independent rat, α-parvalbumin molecules in the crystallographic asymmetric unit, is two to three times higher than the mean coordinate error (0·10 Å), indicating flexibility in the molecule. Sequence differences between α and β-lineage parvalbumins result in repacking of the hydrophobic core and some shifts in the protein backbone. The shifts are localized, however, and entire helices do not shift as rigid units.

Crystal and molecular structure of p-chlorothymols. II: 4-chloro-3-methyl-5-isopropylphenol (PCMT)

The crystal and molecular structure of the title compound: C10H13OCl, determined by single-crystal X-ray diffraction is reported. Crystals are monoclinic, space group P21/a (No14),a=18.435(7),b=24.642(6),c=9.116(6)A,β=103.23(5)°,Z=16,D x =1.216 Mg m−3,F(000)=1568,V=4031(1)A3. The structure was solved by direct methods and the finalR value is 8.5%. The four molecules in asymmetric unit are linked by hydrogen bonds and form an infinite chain parallel to the (bc) plane. Different chains are held together by van der Waals forces.

Molecular and crystal structure of 1-hydroxy-2-methyl-11-methylene-tricyclo (5.3.1.0)2,7-undecan-5-one, C13O2H18

The title compound is orthorhombic witha = 26·132(6),b = 11·023(2),c = 8·317(5), A; space group Iba2;Z = 8,D m = 1·21(1),D c = 1·192 Mg m−3, 1/2(H2O) per molecule in asymmetric unit; λ (MoKα) = 0·7107A; μ = 0·46 cm−1; F(000) = 936. The structure was solved by direct methods and refined to R(F) value of 0·069 using 327 reflections withF ≥ 5σ(F) out of 727 independent reflections for2τ max = 46°. Thetrans fused cyclohexane and cyclohexanone rings form layers along thea-b plane. The axial methyl attached at the bridge-head, interlocks with the translated methylene of the cyclobutane fused across the cyclohexane ring. The equatorial hydroxyl at the bridge-head adjacent to the methyl junction and the water molecule on the two-fold form a water bridge along thez axis. The packing is reminiscent of that observed for the cholesterols used in membrane structure studies.