A. polyphaga mimivirus, the largest known double-stranded DNA virus, is the first virus to exhibit a nucleoside diphosphate kinase gene. The expression and crystallization of the viral NDK are reported.
The complete sequence of the largest known double-stranded DNA virus, Acanthamoeba polyphaga mimivirus, has recently been determined [Raoult et al. (2004 ▶), Science, 306, 1344–1350] and revealed numerous genes not expected to be found in a virus. A comprehensive structural and functional study of these gene products was initiated [Abergel et al. (2005 ▶), Acta Cryst. F61, 212–215] both to better understand their role in the virus physiology and to obtain some clues to the origin of DNA viruses. Here, the preliminary crystallographic analysis of the viral nucleoside diphosphate kinase protein is reported. The crystal belongs to the cubic space group P213, with unit-cell parameter 99.425 Å. The self-rotation function confirms that there are two monomers per asymmetric unit related by a twofold non-crystallographic axis and that the unit cell thus contains four biological entities.
nucleocytoplasmic large DNA virus; NCLDV; nucleoside diphosphate kinase; structural genomics
We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)2
density functional calculations; DNA structures; hydrogen bonds; stacking interactions; Watson–Crick base pairs
Presented is an extension of the CHARMM General force field (CGenFF) to enable the modeling of sulfonyl-containing compounds. Model compounds containing chemical moieties such as sulfone, sulfonamide, sulfonate and sulfamate were used as the basis for the parameter optimization. Targeting high-level quantum mechanical and experimental crystal data, the new parameters were optimized in a hierarchical fashion designed to maintain compatibility with the remainder of the CHARMM additive force field. The optimized parameters satisfactorily reproduced equilibrium geometries, vibrational frequencies, interactions with water, gas phase dipole moments and dihedral potential energy scans. Validation involved both crystalline and liquid phase calculations showing the newly developed parameters to satisfactorily reproduce experimental unit cell geometries, crystal intramolecular geometries and pure solvent densities. The force field was subsequently applied to study conformational preference of a sulfonamide based peptide system. Good agreement with experimental IR/NMR data further validated the newly developed CGenFF parameters as a tool to investigate the dynamic behavior of sulfonyl groups in a biological environment. CGenFF now covers sulfonyl group containing moieties allowing for modeling and simulation of sulfonyl-containing compounds in the context of biomolecular systems including compounds of medicinal interest.
empirical force field; molecular mechanics; molecular dynamics; molecular modeling; potential energy function; sulfonamide; β-strand mimetic; peptidomimetic; medicinal chemistry; drug design
The crystal structure of the title compound [systematic name: 5,6,10-trihydroxy-7-isopropyl-1,1,4a-trimethyl-2,3,4,4a-tetrahydrophenanthren-9(1H)-one], C20H26O4, has been reported previously [Salae et al. (2009 ▶). Acta Cryst. E65, o2379–o2380], but the absolute configuration could not be determined as there was no significant anomalous dispersion using data collected with Mo radiation. The absolute configuration has now been determined by refinement of the Flack parameter with data collected using Cu radiation. The absolute configuration at position 4a of the diterpenoid is (R)-methyl; other features of the molecule and its crystal packing are similar to those previously described.
The title compound, C10H12FN3S, crystallizes in the same space group (P21/c) as two polymorphic forms of 4-phenyl-1-(propan-2-ylidene)thiosemicarbazone [Jian et al. (2005). Acta Cryst. E61, o653–o654; Venkatraman et al. (2005). Acta Cryst. E61, o3914–o3916]. The arrangement of molecules relative to the twofold screw axes is similar to that in the crystal structure of the lower density polymorph. In the solid state, the molecular conformation is stabilized by an intramolecular N—H⋯N hydrogen bond. The molecules form centrosymmetric R
2(8) dimers in the crystal through pairs of N—H⋯S hydrogen bonds.
The crystal structure of the 37.2 kDa At3g21360 gene product from A. thaliana was determined at 2.4 Å resolution. The structure establishes that this protein binds a metal ion and is a member of a clavaminate synthase-like superfamily in A. thaliana.
The crystal structure of the gene product of At3g21360 from Arabidopsis thaliana was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 19.3% (R
free = 24.1%) at 2.4 Å resolution. The crystal structure includes two monomers in the asymmetric unit that differ in the conformation of a flexible domain that spans residues 178–230. The crystal structure confirmed that At3g21360 encodes a protein belonging to the clavaminate synthase-like superfamily of iron(II) and 2-oxoglutarate-dependent enzymes. The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily.
The redetermined structure of title chalcone derivative, C23H16O2, corrects errors in the title, scheme and synthesis in the previous report of the same structure [Jasinski et al. (2011 ▶). Acta Cryst. E67, o795]. There are two independent molecules in the asymmetric unit with slight differences in bond lengths and angles. The dihedral angle between the benzene ring and the anthracene ring system is 73.30 (4)° in one molecule and 73.18 (4)° in the other. Both molecules feature an intramolecular O—H⋯O hydrogen bond, which generates an S(6) ring. In the crystal, molecules are arranged into sheets lying parallel to the ac plane and further stacked along the b axis by π–π interactions with centroid–centroid distances in the range 3.6421 (6)–3.7607 (6) Å. The crystal structure is further stabilized by C—H⋯π interactions. There are also C⋯O [3.2159 (15) Å] short contacts.
The title Schiff base compound, C25H19NO2S, crystallizes in a statistically disordered structure comprising keto and enol tautomeric forms. In the enol form, the benzenoid arrangment is promoted by a strong intramolecular O—H⋯N hydrogen bond and adopts an E conformation about the imine bond. In the keto form there is an intramolecular N—H⋯O hydrogen bond. In the crystal, an extended network of C—H⋯O hydrogen bonds stabilizes columns parallel to the c axis, forming large voids (there are four cavities of 108 Å3 per unit cell) with highly disordered residual electron density. The SQUEEZE procedure in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155] was used to eliminate the contribution of this electron density from the intensity data, and the solvent-free model was employed for the final refinement. The contribution of this undetermined solvent was ignored in the calculation of the unit-cell characteristics.
Corrigendum to Acta Cryst. (2009), E65, o301.
Consideration of a previous unrecognized twinning of the original investigated crystal of the title compound [Kia et al. (2009 ▶). Acta Cryst. E65, o301] led to improved reliability factors and to a slightly higher precision for all geometric parameters. The crystal under investigation was twinned by pseudo-merohedry with [100, 00, 00] as the twin matrix and a refined twin domain fraction of 0.9610 (5):0.0390 (5). The results of the new crystal structure refinement are given here.
The performance of time-dependent density functional theory (TDDFT) for calculations of long-range exciton circular dichroism (CD) is investigated. Tetraphenylporphyrin (TPP) is used as a representative of a class of strongly absorbing chromophores for which exciton CD with chromophore separations of 50 Å and even beyond has been observed experimentally. A dimer model for TPP is set up to reproduce long-range exciton CD previously observed for a brevetoxin derivative. The calculated CD intensity is consistent with TPP separations of over 40 Å. It is found that a hybrid functional with fully long-range corrected range-separated exchange performs best for full TDDFT calculations of the dimer. The range-separation parameter is optimally tuned for TPP, resulting in a good quality TPP absorption spectrum and small DFT delocalization error (measured by the curvature of the energy calculated as a function of fractional electron numbers). Calculated TDDFT data for the absorption spectra of TPP are also used as input for a ‘matrix method’ (MM) model of the exciton CD. For long-range exciton CD, comparison of MM spectra with full TDDFT CD spectra for the dimer shows that the matrix method is capable of producing very accurate results. A MM spectrum obtained from TPP absorption data calculated with the nonhybrid Becke88–Perdew86 (BP) functional is shown to match the experimental brevetoxin spectrum ‘best’, but for the wrong reasons.
ab initio calculations; CD/LC/ORD; density-functional calculations; long-range exciton circular dichroism; porphyrins
A correction is made to the article by Kefala & Weiss [(2006), Acta Cryst. F62, 1116–1119].
A correction is made to the Experimental methods section of the article by Kefala & Weiss [(2006), Acta Cryst. F62, 1116–1119].
dihydrodipicolinate synthase; Mycobacterium tuberculosis; Rv2753c
The angle τ (backbone N—Cα—C) is the most contested Engh and Huber refinement target parameter. It is shown that this parameter is ‘correct’ as a PDB-wide average, but can be improved by taking into account residue types, secondary structures and many other aspects of our knowledge of the biophysical relations between residue type and protein structure.
The Engh and Huber parameters for bond lengths and bond angles have been used uncontested in macromolecular structure refinement from 1991 until very recently, despite critical discussion of their ubiquitous validity by many authors. An extensive analysis of the backbone angle τ (N—Cα—C) illustrates that the Engh and Huber parameters can indeed be improved and a recent study [Tronrud et al. (2010 ▶), Acta Cryst. D66, 834–842] confirms these ideas. However, the present study of τ shows that improving the Engh and Huber parameters will be considerably more complex than simply making the parameters a function of the backbone ϕ, ψ angles. Many other aspects, such as the cooperativity of hydrogen bonds, the bending of secondary-structure elements and a series of biophysical aspects of the 20 amino-acid types, will also need to be taken into account. Different sets of Engh and Huber parameters will be needed for conceptually different refinement programs.
protein structure; protein geometry; stereochemical parameters; restraints; N—Cα—C bond angle
In the title compound, C20H25NO5, the dihydropyridine ring adopts a flattened boat conformation. The methoxyphenyl ring is almost perpendicular to the mean plane of the pyridine ring [dihedral angle = 88.42 (3)°]. The two carbonyl units adopt a synperiplanar conformation with respect to the double bonds in the dihydropyridine ring. In the crystal, molecules are connected by N—H⋯O hydrogen bonds into R
4(24) tetrameric rings. A region of disordered electron density, located at the center of four adjacent molecules, was treated with the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. It is probably the result of traces of the solvent of crystallization and was not taken into account during the structure refinement.
In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I) biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in this study, which are based on The Density Functional Theory (DFT) and time-dependent (TD) DFT. Further, the maximum absorption wavelengths of our theoretical calculations were compared with the experimental data. It was found that the M06/LANL2DZ + DZVP level of calculation provides the best approximation. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT.
molecular structure; absorption spectra; polarizability; chemical reactivity; dipole moment; copper complex; dye-sensitized
The crystal structure of the title compound, C28H18O2, was originally determined by Ehrenberg [(1967 ▶). Acta Cryst. 22, 482–487] using intensity data obtained from Weissenberg photographs. The current determination provides a crystal and molecular structure with a significantly higher precision and presents standard uncertainties on geometric parameters which are not available from the original work. The molecule lies on a crystallographic twofold rotation axis which bisects the C—C bond [1.603 (3) Å] which joins the two anthracen-9(10H)-one units.
The crystal structure of the title compound, C9H10O4, was first reported by Swaminathan, Vimala & Lotter [Acta Cryst. (1976), B32, 1897–1900]. It has been re-examined, improving the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar independent molecule, as the methoxy substituents force the carboxy group to be twisted away from the plane of the aromatic ring by 56.12 (9)°. Due to the antiplanar conformation adopted by the OH group, the molecular components do not form the conventional dimeric units, but are associated in the crystal in chains stabilized by linear O—H⋯O hydrogen bonds, involving the OH groups and the carbonyl O atoms, which form C(3) motifs.
The asymmetric unit of the title compound, C8H8O2, contains two crystallographically independent molecules, which form dimers linked by O⋯H—O hydrogen bonds. The benzene rings in the dimers are inclined at a dihedral angle of 7.30 (8)° and both methyl groups display rotational disorder. This redetermination results in a crystal structure with significantly higher precision than the original determination [Ellas & García-Blanco (1963 ▶). Acta Cryst. 16, 434], in which the authors reported only the unit-cell parameters and space group, without any detailed information on the atomic arrangement. In the crystal, dimers are connected by weak C—H⋯O interactions, forming R
2(10) and R
4(18) rings along  and an infinite zigzag chain of dimers along the  direction also occurs.
Crystals of the title compound, C16H12N2O4, were obtained accidentally by the hydrothermal reaction of 5-[(1H-benzo[d]imidazol-1-yl)methyl]isophthalic acid with manganese chloride tetrahydrate in the presence of KOH as alkaline reagent for the deprotonation. A triclinic polymorph of this structure has been reported previously from a similar reaction [Cheng (2011 ▶). Acta Cryst. E67, o3299]. The benzimidazole ring system is almost planar, with a maximum deviation from the mean plane of 0.020 (4) Å. The benzimidazole unit and benzene ring are inclined at a dihedral angle of 68.17 (4)°, reflecting the axial rotation of the flexible benzimidazolyl arm. In the crystal, pairs of O—H⋯O hydrogen bonds link adjacent molecules into inversion dimers. O—H⋯N contacts connect these dimers into zigzag chains along .