http://journals.iucr.org/d/issues/2008/08/00/isscontsbdy.html Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are papers on crystallographic binding studies, structural analysis of mutants and other structure-function studies. Refinements of previously known structures may be published if sufficient new information is presented. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Papers on the crystallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability. en Copyright (c) 2008 International Union of Crystallography 2008-08-01 International Union of Crystallography International Union of Crystallography http://journals.iucr.org urn:issn:0907-4449 Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are papers on crystallographic binding studies, structural analysis of mutants and other structure-function studies. Refinements of previously known structures may be published if sufficient new information is presented. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Papers on the crystallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability. text/html Acta Crystallographica Section D: Biological Crystallography, Volume 64, Part 8, 2008 text monthly 1 2002-01-01T00:00+00:00 8 64 2008-08-01 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography 815 urn:issn:0907-4449 med@iucr.org August 2008 2008-08-01 http://journals.iucr.org/logos/rss10d.gif http://journals.iucr.org/d/issues/2008/08/00/isscontsbdy.html Still image http://scripts.iucr.org/cgi-bin/paper?hm5062 The enzyme urate oxidase catalyzes the conversion of uric acid to 5-hydroxyisourate, one of the steps in the ureide pathway. Arthrobacter globiformis urate oxidase (AgUOX) was crystallized and structures of crystals soaked in the substrate uric acid, the inhibitor 8-azaxanthin and allantoin have been determined at 1.9–2.2 Å resolution. The biological unit is a homotetramer and two homotetramers comprise the asymmetric crystallographic unit. Each subunit contains two T-fold domains of ββααββ topology, which are usually found in purine- and pterin-binding enzymes. The uric acid substrate is bound tightly to the enzyme by interactions with Arg180, Leu222 and Gln223 from one subunit and with Thr67 and Asp68 of the neighbouring subunit in the tetramer. In the other crystal structures, lithium borate, 8-azaxanthin and allantoate are bound to the enzyme in a similar manner as uric acid. Based on these AgUOX structures, the enzymatic reaction mechanism of UOX has been proposed. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Juan, E.C.M. Hoque, M.M. Shimizu, S. Hossain, M.T. Yamamoto, T. Imamura, S. Suzuki, K. Tsunoda, M. Amano, H. Sekiguchi, T. Takénaka, A. 2008-07-17 doi:10.1107/S0907444908013590 International Union of Crystallography Crystal structures of urate oxidase from A. globiformis and of its complexes with uric acid, allantoate and 8-azaxanthin demonstrate details of substrate recognition and catalysis. en urate oxidase Arthrobacter globiformis uric acid allantoate 8-azaxanthin The enzyme urate oxidase catalyzes the conversion of uric acid to 5-hydroxyisourate, one of the steps in the ureide pathway. Arthrobacter globiformis urate oxidase (AgUOX) was crystallized and structures of crystals soaked in the substrate uric acid, the inhibitor 8-azaxanthin and allantoin have been determined at 1.9–2.2 Å resolution. The biological unit is a homotetramer and two homotetramers comprise the asymmetric crystallographic unit. Each subunit contains two T-fold domains of ββααββ topology, which are usually found in purine- and pterin-binding enzymes. The uric acid substrate is bound tightly to the enzyme by interactions with Arg180, Leu222 and Gln223 from one subunit and with Thr67 and Asp68 of the neighbouring subunit in the tetramer. In the other crystal structures, lithium borate, 8-azaxanthin and allantoate are bound to the enzyme in a similar manner as uric acid. Based on these AgUOX structures, the enzymatic reaction mechanism of UOX has been proposed. text/html Structures of Arthrobacter globiformis urate oxidase–ligand complexes text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 815 822 http://scripts.iucr.org/cgi-bin/paper?hv5107 Identifying the conditions that will produce diffraction-quality crystals can require very many crystallization experiments. The use of robots has increased the number of experiments performed in most laboratories, while in structural genomics centres tens of thousands of experiments can be produced every day. Reliable automated evaluation of these experiments is becoming increasingly important. A more robust classification is achieved by combining different methods of feature extraction with the use of multiple classifiers. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Buchala, S. Wilson, J.C. 2008-07-17 doi:10.1107/S0907444908014273 International Union of Crystallography Improved classification of images from crystallization experiments is obtained using multiple classifiers to combine different feature-extraction methods. en crystallization image classification Identifying the conditions that will produce diffraction-quality crystals can require very many crystallization experiments. The use of robots has increased the number of experiments performed in most laboratories, while in structural genomics centres tens of thousands of experiments can be produced every day. Reliable automated evaluation of these experiments is becoming increasingly important. A more robust classification is achieved by combining different methods of feature extraction with the use of multiple classifiers. text/html Improved classification of crystallization images using data fusion and multiple classifiers text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 823 833 http://scripts.iucr.org/cgi-bin/paper?dz5131 A pattern-recognition-based method for the detection of planar objects in protein or DNA/RNA crystal structure determination is described. The procedure derives a set of rotation-invariant numeric features from local regions in the asymmetric unit of a crystallographic electron-density map. These features, primarily moments of various orders, capture different aspects of the local shape of objects in the electron density. Feature classification is achieved using a linear discriminant that is trained to optimize the contrast between planar and nonplanar objects. In five selected test cases with X-ray data spanning 2.0–3.0 Å resolution, the procedure identified the correct location and orientation for almost all of the double-ring and a majority of the single-ring planar groups. The accuracy of the location of the plane centres is of the order of 0.5 Å, even in moderately noisy density maps. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Hattne, J. Lamzin, V.S. 2008-07-17 doi:10.1107/S0907444908014327 International Union of Crystallography A pattern-recognition-based method for the identification of planar objects in crystallographic electron-density maps is presented. The accuracy of the located centres of the planes is of the order of 0.5 Å. en pattern recognition electron-density maps detection of planar objects A pattern-recognition-based method for the detection of planar objects in protein or DNA/RNA crystal structure determination is described. The procedure derives a set of rotation-invariant numeric features from local regions in the asymmetric unit of a crystallographic electron-density map. These features, primarily moments of various orders, capture different aspects of the local shape of objects in the electron density. Feature classification is achieved using a linear discriminant that is trained to optimize the contrast between planar and nonplanar objects. In five selected test cases with X-ray data spanning 2.0–3.0 Å resolution, the procedure identified the correct location and orientation for almost all of the double-ring and a majority of the single-ring planar groups. The accuracy of the location of the plane centres is of the order of 0.5 Å, even in moderately noisy density maps. text/html Pattern-recognition-based detection of planar objects in three-dimensional electron-density maps text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 834 842 http://scripts.iucr.org/cgi-bin/paper?yt5006 Few examples of macromolecular crystals containing lattice-translocation defects have been published in the literature. Lattice translocation and twinning are believed to be two common but different crystal-growth anomalies. While the successful use of twinned data for structure determination has become relatively routine in recent years, structure determination of crystals with lattice-translocation defects has not often been reported. To date, only four protein crystal structures containing such a crystal defect have been determined, using corrected, but not uncorrected, intensity data. In this report, the crystallization, structure determination and refinement of N1 neuraminidase derived from the 1918 H1N1 influenza virus (18NA) at 1.65 Å resolution are described. The crystal was indexed in space group C2221, with unit-cell parameters a = 117.7, b = 138.5, c = 117.9 Å, and the structure was solved by molecular replacement. The lattice-translocation vector in the 18NA crystal was (0, 1/2, 1/2) or its equivalent vector (1/2, 0, 1/2) owing to the C lattice symmetry. Owing to this special lattice-translocation vector in space group C2221, structure refinement could be achieved in two different ways: using corrected or uncorrected diffraction data. In the refinement with uncorrected data, a composite model was built to represent the molecules in the translated and untranslated layers, respectively. This composite structure model provided a unique example to examine how the molecules were arranged in the two lattice domains resulting from lattice-translocation defects. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Zhu, X. Xu, X. Wilson, I.A. 2008-07-17 doi:10.1107/S0907444908016648 International Union of Crystallography The structure of the 1918 H1N1 neuraminidase was determined to 1.65 Å from crystals with a lattice-translocation defect using uncorrected, as well as corrected, diffraction data. en neuraminidases crystal defects lattice translocation pseudo-translation residual electron density Few examples of macromolecular crystals containing lattice-translocation defects have been published in the literature. Lattice translocation and twinning are believed to be two common but different crystal-growth anomalies. While the successful use of twinned data for structure determination has become relatively routine in recent years, structure determination of crystals with lattice-translocation defects has not often been reported. To date, only four protein crystal structures containing such a crystal defect have been determined, using corrected, but not uncorrected, intensity data. In this report, the crystallization, structure determination and refinement of N1 neuraminidase derived from the 1918 H1N1 influenza virus (18NA) at 1.65 Å resolution are described. The crystal was indexed in space group C2221, with unit-cell parameters a = 117.7, b = 138.5, c = 117.9 Å, and the structure was solved by molecular replacement. The lattice-translocation vector in the 18NA crystal was (0, 1/2, 1/2) or its equivalent vector (1/2, 0, 1/2) owing to the C lattice symmetry. Owing to this special lattice-translocation vector in space group C2221, structure refinement could be achieved in two different ways: using corrected or uncorrected diffraction data. In the refinement with uncorrected data, a composite model was built to represent the molecules in the translated and untranslated layers, respectively. This composite structure model provided a unique example to examine how the molecules were arranged in the two lattice domains resulting from lattice-translocation defects. text/html Structure determination of the 1918 H1N1 neuraminidase from a crystal with lattice-translocation defects text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 843 850 http://scripts.iucr.org/cgi-bin/paper?gx5126 An extremely low-field signal (at approximately 18 p.p.m.) in the 1H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental 1H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 Å resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 Å) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor–acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pKa values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are all located close to the active site and short interactions between Ser and Thr side-chain OH groups and backbone carbonyl O atoms seem to play an important role in the stability of the protein structure. These results illustrate the significance of short strong hydrogen bonds in proteins. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Langkilde, A. Kristensen, S.M. Lo Leggio, L. Mølgaard, A. Jensen, J.H. Houk, A.R. Navarro Poulsen, J.-C. Kauppinen, S. Larsen, S. 2008-07-17 doi:10.1107/S0907444908017083 International Union of Crystallography The short hydrogen bonds in rhamnogalacturonan acetylesterase have been investigated by structure determination of an active-site mutant, 1H NMR spectra and computational methods. Comparisons are made to database statistics. A very short carboxylic acid carboxylate hydrogen bond, buried in the protein, could explain the low-field (18 p.p.m.) 1H NMR signal. en short hydrogen bonds low-field NMR signals rhamnogalacturonan acetylesterase An extremely low-field signal (at approximately 18 p.p.m.) in the 1H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental 1H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 Å resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 Å) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor–acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pKa values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are all located close to the active site and short interactions between Ser and Thr side-chain OH groups and backbone carbonyl O atoms seem to play an important role in the stability of the protein structure. These results illustrate the significance of short strong hydrogen bonds in proteins. text/html Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 851 863 http://scripts.iucr.org/cgi-bin/paper?wd5096 The recently discovered charge-flipping phasing algorithm has received growing interest in small-molecule crystallography and powder diffraction. This computational methodology differs from classical direct methods as it does not require a priori knowledge of either space-group symmetry or chemical composition and does not rely on probabilistic phase relations. Here, it is shown that the charge-flipping algorithm is capable of solving large macromolecular structures with up to ∼6000 atoms in the asymmetric unit using suitable normalized intensity data at atomic resolution (∼1.0 Å). Moreover, it is demonstrated that this algorithm also provides an efficient tool for the experimental phasing of highly complex heavy-atom or anomalous scattering substructures at medium to low resolution (∼2–6 Å) that are frequently difficult to determine using Patterson techniques or direct methods. With the present extension to macromolecular crystallography, charge flipping has proved to be a very well performing and general phase-recovery algorithm in all fields of kinematical diffraction. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Dumas, C. van der Lee, A. 2008-07-17 doi:10.1107/S0907444908017381 International Union of Crystallography A novel phasing method that uses the charge-flipping algorithm has been used to solve the ab initio structure of biological macromolecules at atomic resolution and to determine heavy-atom or anomalous scattering substructures. en charge flipping substructure solution ab initio phasing The recently discovered charge-flipping phasing algorithm has received growing interest in small-molecule crystallography and powder diffraction. This computational methodology differs from classical direct methods as it does not require a priori knowledge of either space-group symmetry or chemical composition and does not rely on probabilistic phase relations. Here, it is shown that the charge-flipping algorithm is capable of solving large macromolecular structures with up to ∼6000 atoms in the asymmetric unit using suitable normalized intensity data at atomic resolution (∼1.0 Å). Moreover, it is demonstrated that this algorithm also provides an efficient tool for the experimental phasing of highly complex heavy-atom or anomalous scattering substructures at medium to low resolution (∼2–6 Å) that are frequently difficult to determine using Patterson techniques or direct methods. With the present extension to macromolecular crystallography, charge flipping has proved to be a very well performing and general phase-recovery algorithm in all fields of kinematical diffraction. text/html Macromolecular structure solution by charge flipping text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 864 873 http://scripts.iucr.org/cgi-bin/paper?mv5020 A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Lawson, C.L. Dutta, S. Westbrook, J.D. Henrick, K. Berman, H.M. 2008-07-17 doi:10.1107/S0907444908017393 International Union of Crystallography A new data model for PDB entries of viruses and other biological assemblies with regular noncrystallographic symmetry is described. en virus structures Protein Data Bank database integration uniform curation point symmetry helical symmetry biological assemblies A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive. text/html Representation of viruses in the remediated PDB archive text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 874 882 http://scripts.iucr.org/cgi-bin/paper?hv5109 Dihydroflavonol 4-reductase (DFR) is a key enzyme of the flavonoid biosynthesis pathway which catalyses the NADPH-dependent reduction of 2R,3R-trans-dihydroflavonols to leucoanthocyanidins. The latter are the precursors of anthocyans and condensed tannins, two major classes of phenolic compounds that strongly influence the organoleptic properties of wine. DFR has been investigated in many plant species, but little was known about its structural properties until the three-dimensional structure of the Vitis vinifera enzyme complexed with NADP+ and its natural substrate dihydroquercetin (DHQ) was described. In the course of the study of substrate specificity, crystals of DFR–NADP+–flavonol (myricetin and quercetin) complexes were obtained. Their structures exhibit major changes with respect to that of the abortive DFR–NADP+–DHQ complex. Two flavonol molecules bind to the catalytic site in a stacking arrangement and alter its geometry, which becomes incompatible with enzymatic activity. The X-ray structures of both DFR–NADP+–myricetin and DFR–NADP+–quercetin are reported together with preliminary spectroscopic data. The results suggest that flavonols could be inhibitors of the activity of DFR towards dihydroflavonols. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Trabelsi, N. Petit, P. Manigand, C. Langlois d'Estaintot, B. Granier, T. Chaudière, J. Gallois, B. 2008-07-17 doi:10.1107/S0907444908017769 International Union of Crystallography Structures of grape dihydroflavonol 4-reductase in complex with NADP+ and various flavonols suggest possible inhibition of the enzyme by flavonols. Initial kinetics experiments confirmed the inhibition and showed its competitive character. en flavonoid biosynthesis short-chain dehydrogenase reductases enzyme–ligand complexes flavonols Dihydroflavonol 4-reductase (DFR) is a key enzyme of the flavonoid biosynthesis pathway which catalyses the NADPH-dependent reduction of 2R,3R-trans-dihydroflavonols to leucoanthocyanidins. The latter are the precursors of anthocyans and condensed tannins, two major classes of phenolic compounds that strongly influence the organoleptic properties of wine. DFR has been investigated in many plant species, but little was known about its structural properties until the three-dimensional structure of the Vitis vinifera enzyme complexed with NADP+ and its natural substrate dihydroquercetin (DHQ) was described. In the course of the study of substrate specificity, crystals of DFR–NADP+–flavonol (myricetin and quercetin) complexes were obtained. Their structures exhibit major changes with respect to that of the abortive DFR–NADP+–DHQ complex. Two flavonol molecules bind to the catalytic site in a stacking arrangement and alter its geometry, which becomes incompatible with enzymatic activity. The X-ray structures of both DFR–NADP+–myricetin and DFR–NADP+–quercetin are reported together with preliminary spectroscopic data. The results suggest that flavonols could be inhibitors of the activity of DFR towards dihydroflavonols. text/html Structural evidence for the inhibition of grape dihydroflavonol 4-reductase by flavonols text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 883 891 http://scripts.iucr.org/cgi-bin/paper?dz5133 Superoxide dismutase (SOD) plays a central role in cellular defence against oxidative stress and is of pharmaceutical importance. The SOD from Potentilla atrosanguinea (Pa-SOD) is a unique enzyme as it possesses free-radical scavenging capability at temperatures ranging between 263 and 353 K. The crystal structure of recombinant Pa-SOD has been determined to 2.3 Å resolution. The active-site residues are well ordered and additional water molecules are present in place of a bound copper ion. There is a significant difference in the relative orientation of the two subunits of Pa-SOD and asymmetry is also present in numerous hydrogen-bonding interactions. Structures of SODs, both bound with copper and unbound, have been compared with respect to the orientation of the electrostatic and Greek-key loops. This analysis provides new insights into the copper-chelation process in SODs. Several new structural features in Pa-SOD which may be responsible for its unique properties of thermostability and expanded range of antioxidant activity are also highlighted. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Yogavel, M. Mishra, P.C. Gill, J. Bhardwaj, P.K. Dutt, S. Kumar, S. Ahuja, P.S. Sharma, A. 2008-07-17 doi:10.1107/S0907444908019069 International Union of Crystallography Structural insights were obtained into the copper-chelation mechanism in superoxide dismutases. en copper binding dismutases free radicals high altitude thermostability Superoxide dismutase (SOD) plays a central role in cellular defence against oxidative stress and is of pharmaceutical importance. The SOD from Potentilla atrosanguinea (Pa-SOD) is a unique enzyme as it possesses free-radical scavenging capability at temperatures ranging between 263 and 353 K. The crystal structure of recombinant Pa-SOD has been determined to 2.3 Å resolution. The active-site residues are well ordered and additional water molecules are present in place of a bound copper ion. There is a significant difference in the relative orientation of the two subunits of Pa-SOD and asymmetry is also present in numerous hydrogen-bonding interactions. Structures of SODs, both bound with copper and unbound, have been compared with respect to the orientation of the electrostatic and Greek-key loops. This analysis provides new insights into the copper-chelation process in SODs. Several new structural features in Pa-SOD which may be responsible for its unique properties of thermostability and expanded range of antioxidant activity are also highlighted. text/html Structure of a superoxide dismutase and implications for copper-ion chelation text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 892 901 http://scripts.iucr.org/cgi-bin/paper?dz5129 The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and 2j4y; space group P31) can be re-interpreted as hexagonal (space group P64). Two molecules of the G protein-coupled receptor are present in the asymmetric unit in the trigonal models. However, the noncrystallographic twofold axes parallel to the c axis can be treated as crystallographic symmetry operations in the hexagonal space group. This halves the asymmetric unit and makes all of the protein molecules equivalent in these structures. Corrections for merohedral twinning were also applied in the refinement in the higher symmetry space group for one of the structures (2j4y). Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Stenkamp, R.E. 2008-07-17 doi:10.1107/S0907444908017162 International Union of Crystallography Two crystal structures of rhodopsin that were originally described using trigonal symmetry can be interpreted in a hexagonal unit cell with a smaller asymmetric unit. en alternate space groups rhodopsin G protein-coupled receptors integral membrane proteins The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and 2j4y; space group P31) can be re-interpreted as hexagonal (space group P64). Two molecules of the G protein-coupled receptor are present in the asymmetric unit in the trigonal models. However, the noncrystallographic twofold axes parallel to the c axis can be treated as crystallographic symmetry operations in the hexagonal space group. This halves the asymmetric unit and makes all of the protein molecules equivalent in these structures. Corrections for merohedral twinning were also applied in the refinement in the higher symmetry space group for one of the structures (2j4y). text/html Alternative models for two crystal structures of bovine rhodopsin text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography short communications 902 904 http://scripts.iucr.org/cgi-bin/paper?be5104 The crystal-packing and cohesive energies in the structures of two polymorphs of the title tetrapeptide have been analyzed using molecule–molecule energies calculated using the PIXEL method. Coulombic energies are non-empirical and are much more accurate than those calculated using point-charge methods. The results explain and rationalize the cohesion and mutual recognition of these peptide molecules, with a clear distinction between polar and dispersive contributions, shedding light on subtle differences between polymorphic arrangements. For systems of the present size, the necessary calculations can be carried out on a personal computer and require quite acceptable computing times. Although an extension to larger peptides is problematic for obvious reasons, it is suggested that this type of analysis could be a valuable and practical tool in the understanding of the principles of peptide aggregation. Copyright (c) 2008 International Union of Crystallography urn:issn:0907-4449 Gavezzotti, A. 2008-07-17 doi:10.1107/S0907444908018568 International Union of Crystallography The crystal-packing and cohesive energies in the structures of two polymorphs of the title tetrapeptide have been analyzed using molecule–molecule energies calculated using the PIXEL method. en PIXEL NNQQ crystal polymorphs peptide aggregation intermolecular energies The crystal-packing and cohesive energies in the structures of two polymorphs of the title tetrapeptide have been analyzed using molecule–molecule energies calculated using the PIXEL method. Coulombic energies are non-empirical and are much more accurate than those calculated using point-charge methods. The results explain and rationalize the cohesion and mutual recognition of these peptide molecules, with a clear distinction between polar and dispersive contributions, shedding light on subtle differences between polymorphic arrangements. For systems of the present size, the necessary calculations can be carried out on a personal computer and require quite acceptable computing times. Although an extension to larger peptides is problematic for obvious reasons, it is suggested that this type of analysis could be a valuable and practical tool in the understanding of the principles of peptide aggregation. text/html Coulombic and dispersive factors in the molecular recognition of peptides: PIXEL calculations on two NNQQ (Asn-Asn-Gln-Gln) crystal polymorphs text 8 64 2008-07-17 Copyright (c) 2008 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography short communications 905 908