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Crystallographic Data (crystallographic + data)
Kinds of Crystallographic Data Selected AbstractsNovel Cadmium(II) Adipate Coordination Polymers with Structural Transformation via Oxalate Ligand: Syntheses, Structures and Fluorescence PropertiesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 20 2004Na Hao Abstract Two novel cadmium adipate coordination polymers [Cd{O2C(CH2)4CO2}{1,10-phen}]n (1) and [Cd2(C2O4){O2C(CH2)4CO2(OH2)2}{2,2,-bipy}]·H2O (2) [adipic acid = HO2C(CH2)4CO2H] have been hydrothermally synthesized and characterized by elemental analyses, IR spectroscopy, thermogravimetric analysis and single-crystal X-ray diffraction. Crystallographic data for 1: monoclinic, C2/c, a = 16.186(3) Å, b = 15.487(3) Å, c = 14.052(3) Å, , = 112.73(3)°, Z = 8. Crystal data for 2: monoclinic, Cc, a = 23.448(5) Å, b = 11.826(2) Å, c = 8.3163(17) Å, , = 99.08(3)°, Z = 4. The structural analysis reveals that 1 forms a novel one-dimensional chain in which the binuclear Cd centers are linked by adipate anions. Compound 2 is the first example in which both a 2,2,-bipy ligand and an oxalate group are found in the {M/adipate} system. Compound 2 possesses one-dimensional sine- or cosine-type chains, which are alternately connected together by the oxalate group to form a three-dimensional framework. The structural determination reveals that the introduction of the oxalate ligand causes the dimensional transformation of the compounds. Compounds 1 and 2 show strong fluorescent properties at room temperature. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Free radical 4-nitrophenylation of thieno[2,3- b]pyridine.JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 1 2001Part 2: Isolation, structural studies of three samples of mono (4-nitrophenyl) products; relative yields of the five possible isomers From the crude mixtures of isomeric 4-nitrophenylthieno[2,3- b]pyridines (3) previously reported [1] were isolated three analytically pure samples, viz. the 2-isomer (yellow needles, mp 258°, 3a), the 6-isomer (red prisms, mp 182°, 3e), and a ternary mixture of the 2-, 3-, and 4-isomers (orange needles, mp 213°, 3a:3b:3c = 1.3:1.0:0.5). The 258° compound was identified as either 3a or 3b by its 1H nmr spectrum and definitively as the former by its x-ray crystallographic analysis. The isomeric identities of the 182° and 213° samples were established from their 1H nmr spectra only. No 5-isomer (3d) was identified. Semi-quantitatively, relative isomeric yields fit the pattern 2- (64%)>>6- (14%),3- (12%)>4- (6%),5-(,4%). Crystallographic data for 3a are presented. [source] Monohalogenated ferrocenes C5H5FeC5H4X (X = Cl, Br and I) and a second polymorph of C5H5FeC5H4IACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009Alexander S. Romanov The structures of the three title monosubstituted ferrocenes, namely 1-chloroferrocene, [Fe(C5H5)(C5H4Cl)], (I), 1-bromoferrocene, [Fe(C5H5)(C5H4Br)], (II), and 1-iodoferrocene, [Fe(C5H5)(C5H4I)], (III), were determined at 100,K. The chloro- and bromoferrocenes are isomorphous crystals. The new triclinic polymorph [space group P, Z = 4, T = 100,K, V = 943.8,(4),Å3] of iodoferrocene, (III), and the previously reported monoclinic polymorph of (III) [Laus, Wurst & Schottenberger (2005). Z. Kristallogr. New Cryst. Struct.220, 229,230; space group Pc, Z = 4, T = 100,K, V = 924.9,Å3] were obtained by crystallization from ethanolic solutions at 253 and 303,K, respectively. All four phases contain two independent molecules in the unit cell. The relative orientations of the cyclopentadienyl (Cp) rings are eclipsed and staggered in the independent molecules of (I) and (II), while (III) demonstrates only an eclipsed conformation. The triclinic and monoclinic polymorphs of (III) contain nonbonded intermolecular I...I contacts, causing different packing modes. In the triclinic form of (III), the molecules are arranged in zigzag tetramers, while in the monoclinic form the molecules are arranged in zigzag chains along the a axis. Crystallographic data for (III), along with the computed lattice energies of the two polymorphs, suggest that the monoclinic form is more stable. [source] Life-science applications of the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 6-1 2002Robin Taylor Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling of in vivo situations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary to in vacuo theoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein,ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding `hot spots' on proteins, docking ligands into enzyme active sites, de novo ligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules. [source] Synthesis and Structures of Lanthanide Complexes of N - p -Tolylsulfonylglycinate and 1,10-PhenanthrolineCHINESE JOURNAL OF CHEMISTRY, Issue 9 2005Man-Bo Zhang Abstract Three new lanthanide complexes with the formulae [Eu2(TsGly) 6(phen) 2(H2O) 2] (1), [Ln(TsGly) 2(phen) 2(H2O) 2]Cl·2H2O [Ln=Er (2a) and Yb (2b), TsGlyN - p -tolylsulfonylglycinate, phen1,10-phenanthroline] were synthesized. Crystallographic data for 1: monoclinic, P21/n, a=1.29791(16) nm, b&=1.9034(2) nm, c=1.7596(2) nm, ,=93.410(3) °, V=4.3394(9) nm3, Z=4, R1=0.0326, wR2=0.0771; and for 2b: triclinic, P1, a=1.2674(2) nm, b=1.4405(2) nm, c=1.4809(3) nm, ,=113.256(3) °, ,=108.253(3) °, ,=94.739(3) °, V=2.2922(7) nm3, Z2,R1=0.0292, w R2=0.0669. X-ray diffractional analysis reveals that compound 1 adopts dinuclear structure with fourfold bridging TsGly ligands between the Eu(III) centers, while compound 2b features an unusual mononuclear structure. [source] A three-dimensional model of the U1 small nuclear ribonucleoprotein particleENTOMOLOGICAL RESEARCH, Issue 2 2010Jason A. SOMARELLI Abstract Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5, exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes. [source] Do Metal,Metal Multiply-Bonded "Ligands" Have a trans Influence?EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 36 2008Magnetic Comparisons of Heterometallic CrCr···Co, MoMo···Co Interactions, Structural Abstract Reported here are two new compounds containing either a CrCr···Co [1, CrCrCo(dpa)4Cl2, dpa = 2,2,-dipyridylamide] or a MoMo···Co [2, MoMoCo(dpa)4Cl2] framework both having a multiply-bonded unit (CrCr in 1, MoMo in 2) in close proximity to the Co2+ ion and trans to a Co,Cl bond. Variable temperature magnetic susceptibility measurements reveal 1 to have a temperature-dependent spin equilibrium between a low-spin (S = 1/2) and high-spin (S = 3/2) state, whereas the Co2+ ion in 2 exists solely in its high-spin state. The crystal structures of 1 and 2 were determined. Variable temperature crystallographic data of 1 at 100 K and at room temperature reveal that the spin-transition affects not only the Co,ligand bond lengths but also the terminal Cr,ligand bond lengths. Whereas the Cr···Co distance becomes shorter by 0.13 Å in the low-spin form, the Co,Cldistance becomes longer by 0.2 Å. These observations,along with the crystal structure of 2, suggest that the multiply-bonded MM group has a trans influence on the Co2+ ion.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] New 4,-Functionalized 2,2,:6,,2,,-Terpyridines for Applications in Macromolecular Chemistry and NanoscienceEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 19 2003Philip R. Andres Abstract The well-known reaction of 4,-chloro-2,2,:6,,2,,-terpyridine with alkoxide nucleophiles leads to 4,-functionalized 2,2,:6,,2,,-terpyridines. This reaction allows the easy introduction of different functional groups onto the terpyridine at the 4,-position, i.e. opposite to the metal binding site, in one reaction step. Among the functionalized 2,2,:6,,2,,-terpyridines reported here are amines (including chiral examples), carboxylic acids, simple alkoxy-chain terpyridines with different chain lengths, and a stilbene-functionalized terpyridine. Moreover, the synthesis of two important already known substances was significantly improved. One example of a sequential functionalization of the (aminopentoxy)terpyridine with a dithiolane functionality is also reported. For two of the alkyl-chain-functionalized terpyridines, single-crystal X-ray crystallographic data were obtained. Finally, ordered monolayers of alkyl-substituted terpyridines on HOPG were visualized using STM. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Mechanism of H-8 inhibition of Cyclin-dependent kinase 9: study using inhibitor-immobilized matricesGENES TO CELLS, Issue 3 2003Daisuke Shima Background: Positive transcription elongation factor b (P-TEFb), which phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAPII), is comprised of the catalytic subunit cyclin-dependent kinase 9 (CDK9) and the regulatory subunit cyclin T. The kinase activity and transcriptional activation potential of P-TEFb is sensitive to various compounds, including H-8, 5,6-dichloro-1-,-d-ribofuranosylbenzimidazole (DRB), and flavopiridol. Results: We investigated the molecular mechanism of the H-8 inhibition of CDK9 using matrices to which H-9, an amino derivative of H-8, was immobilized. CDK9 bound specifically to H-9, and this interaction was competitively inhibited by ATP and DRB, but not by flavopiridol. Mutational analyses demonstrated that the central region of CDK9, which encompasses the T-loop region, was important for its binding to H-9. Conclusions: H-9-immobilized latex beads are useful for trapping CDK9 and a subset of kinases from crude cell extracts. The flavopiridol-binding region of CDK9 is most likely different from its H-9-binding region. These biochemical data support previously reported observations which were based on crystallographic data. [source] Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2001Tran Trung Tran Abstract When a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio-substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp2 sulfur are required. In this article, parameters for the thioamide group have been derived for the molecular mechanics CFF91 force field (available at http://www.ludwig.edu.au/archive/tran). The bond increment charges were obtained by fitting to ab initio charges and dipoles. The van der Waals parameters were obtained by fitting to high-resolution crystallographic data, and the nonbonded parameters were verified by comparing with experimentally derived lattice energy. The bonded parameters were derived by least-square fits to the ab initio calculated energy surfaces, i.e., conformational energy as well as their first and second derivatives of seven model thioamide molecules. When the sp2 sulfur parameters were tested on a set of seven X-ray crystallographic structures from the Cambridge Structural Database, they satisfactorily reproduced the bond lengths, bond angles, torsional angles, and nonbonded distances of all the crystal structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1010,1025, 2001 [source] When epitaxy controls garnet growthJOURNAL OF METAMORPHIC GEOLOGY, Issue 4 2007R. SPIESS Abstract Within a mica schist from the coesite-bearing Brossasco-Isasca Unit (Western Alps), microstructural analysis shows that Alpine garnet grains are aligned with the crenulated foliation. Garnet crystallographic orientation was analysed with electron backscatter diffraction (EBSD): the obtained crystallographic dispersion patterns and distribution patterns of misorientation axes suggest a strong parallelism of {110} garnet planes with a 56°W-dipping foliation. The data are interpreted as evidence for an epitaxial growth of garnet upon (001) biotite planes, sometime during and/or after dispersion of the biotite/garnet crystals from their initially foliation-parallel orientation by rotation about the Alpine crenulation axis. This interpretation is based on the comparison of the measured EBSD data with: (i) theoretical dispersion trajectories of garnet crystallographic data, (ii) numerically modelled pole figures, and (iii) numerically modelled misorientation axis distribution patterns. Our data suggest that epitaxial growth of garnet upon biotite is allowed by distortion of the pseudohexagonal basal oxygen ring structure on (001) biotite surfaces, and that distortion is driven by introduction of missing ions. Our data further suggest that the spatial distribution of precursor phases influences the distribution patterns of garnet within mica schists. [source] The integration of experimental in-situ EBSD observations and numerical simulations: a novel technique of microstructural process analysisJOURNAL OF MICROSCOPY, Issue 3 2004S. Piazolo Summary The combination of subgrain- and grain-scale microstructural data collected during in-situ heating experiments and numerical simulations of equivalent microstructural development offers an innovative and powerful tool in the advancement of the understanding of microstructural processes. We present a system that fully integrates subgrain- to grain-scale crystallographic data obtained during in-situ observations during heating experiments in a scanning electron microscope and the two-dimensional hybrid numerical modelling system Elle. Such a system offers the unique opportunity to test and verify theories for microstructural development, as predictions made by numerical simulations can be directly coupled to appropriate physical experiments and, conversely, theoretical explanations of experimental observations should be testable with numerical simulations. Discrepancies between data obtained with both techniques suggest the need for an in-depth investigation and thus open up new avenues of theory development, modification and verification. In addition, because in numerical models it is possible to select the processes modelled, the effect of individual processes on the microstructural development of a specific material can be quantified. To illustrate the potential and methodology of the so-called EBSD2Elle system, two in-situ experiments and their equivalent numerical experiments are presented. These are static heating experiments of (a) an annealed Ni-foil coupled with a front tracking model for grain growth and (b) a cold deformed rock salt with kinetic Monte Carlo simulations for subgrain growth. [source] Thioenols and thioamides substituted by two , -EWGs.JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2008Comparison with analogous amides, enols Abstract Condensation of organic isothiocyanates with active methylene compounds gave nine thioamides RNHCSCHYY, or their isomeric thioenols RNHC(SH),=,CYY, for substrates in which Y and Y, are electron-withdrawing groups (EWG). These included derivatives of Meldrum's acid (MA) which showed 100% thioenol in all solvents. For other compounds the percentages of thioenol in CDCl3 when R,=,Ph are 100% when Y,=,CN and Y,,=,CO2Me or Y,,=,CO2CH2CCl3, 6% when Y,=,Y,,=,CO2CH2CF3, and 0% when Y,=,Y,,=,CO2Me. The chemical shift of SH (highest values 12.0,16.0,ppm) served as a probe for the thioenol structures and also for the extent of hydrogen bonding to the SH group. In contrast to simple ketones and thioketones in which thioenolization is favored over enolization by factors as large as 106, for intramolecular competition KThioenol/KEnol ratios are much lower than for systems not substituted by , -EWGs. X-ray crystallography of the 5-anilido-MA derivative shows a hydrogen-bonded thioenol structure. ,(OH), ,(NH), KEnol, and crystallographic data for analogous thioenol and enol systems are compared. Copyright © 2008 John Wiley & Sons, Ltd. [source] 4d Electronic structure analysis of ruthenium in the perovskite oxides by Ru K - and L -edge XASJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2001Jong-Young Kim The 4d electronic structure of ruthenium in the perovskite oxides, La2MRuIVO6 (M = Zn, Mg, and Li) and Ba2YRuVO6, has been investigated by the Ru K-and L-edge XANES and EXAFS analyses. Such X-ray absorption spectroscopic results clarify that the RuIV (d4) and RuV (d3) ions are stabilized in nearly regular Oh site. Comparing the Ru L-edge XANES spectra of perovskites containing isovalent ruthenium, it has been found that the t2g state is mainly influenced by A site cation, whereas the eg is mainly affected by neighboring B site cation. The experimental EXAFS spectra in the range of R ,,4.5 Å are well reproduced by ab-initio calculation based on crystallographic data, which supports the long-range structure presented by Rietveld refinement. [source] New insights into the active site structure and catalytic mechanism of tyrosinase and its related proteinsPIGMENT CELL & MELANOMA RESEARCH, Issue 6 2009Concepcion Olivares Summary Tyrosinases are widely distributed in nature. They are copper-containing oxidases belonging to the type 3 copper protein family, together with catechol oxidases and haemocyanins. Tyrosinases are essential enzymes in melanin biosynthesis and therefore responsible for pigmentation of skin and hair in mammals, where two more enzymes, the tyrosinase-related proteins (Tyrps), participate in the pathway. The structure and catalytic mechanism of mammalian tyrosinases have been extensively studied but they are not completely understood because of the lack of information on the tertiary structure. The availability of crystallographic data of one plant catechol oxidase and one bacterial tyrosinase has improved the model of the three-dimensional structure of the active site of the enzyme. Furthermore, sequence comparison of tyrosinase and the Tyrps reveals that the three orthologue proteins share many key structural features, because of their common origin from an ancestral gene, although the specific residues responsible for their different catalytic capabilities have not been identified yet. This review summarizes our current knowledge of tyrosinase and Tyrps structure and function and describes the catalytic mechanism of tyrosinase and Dct/Tyrp2, which are better characterized. [source] Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scatteringPROTEIN SCIENCE, Issue 4 2009Pau Bernadó Abstract Signal transducer and activator of transcription (STAT) proteins play a crucial role in the activation of gene transcription in response to extracellular stimuli. The regulation and activity of these proteins require a complex rearrangement of the domains. According to the established models, based on crystallographic data, STATs convert from a basal antiparallel inactive dimer into a parallel active one following phosphorylation. The simultaneous analysis of small-angle X-ray scattering data measured at different concentrations of unphosphorylated human STAT5a core domain unambiguously identifies the simultaneous presence of a monomer and a dimer. The dimer is the minor species but could be structurally characterized by SAXS in the presence of the monomer using appropriate computational tools and shown to correspond to the antiparallel assembly. The equilibrium is governed by a moderate dissociation constant of Kd , 90 ,M. Integration of these results with previous knowledge of the N-terminal domain structure and dissociation constants allows the modeling of the full-length protein. A complex network of intermolecular interactions of low or medium affinity is suggested. These contacts can be eventually formed or broken to trigger the dramatic modifications in the dimeric arrangement needed for STAT regulation and activity. [source] Centrosymmetric and pseudo-centrosymmetric structures refined as non-centrosymmetricACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2006H. D. Flack The behaviour of the Flack parameter for centrosymmetric and pseudo-centrosymmetric crystal structures based on crystal structures published as being non-centrosymmetric is presented. It is confirmed for centrosymmetric structures that the value obtained for the Flack parameter is critically dependent on the Friedel coverage of the intensity data, approaching 0.5 for a coverage of 100% and sticking near the starting value for a coverage of 0%. For pseudo-centrosymmetric structures, even those very close to being centrosymmetric, it is found that it is often possible to obtain significant values of the Flack parameter. A theoretical basis for this surprising result is established. It has also been possible to establish an a priori estimate of the standard uncertainty of the Flack parameter based only on the chemical composition of the compound and the wavelength of the radiation. The paper concludes with preliminary presentations of bias in the Flack parameter and of inconsistent chemical and crystallographic data. [source] Azetidine, pyrrolidine and hexamethyleneimine at 170,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2008Andrew D. Bond The crystal structures of the cyclic amines azetidine (C3H7N), pyrrolidine (C4H9N) and hexamethyleneimine (homopiperidine, C6H13N), of the series (CH2)nNH, with n = 3, 4 and 6, respectively, have been determined at 170,K, following in situ crystallization from the melt. These structures provide crystallographic data to complete the homologous series of cyclic amines (CH2)nNH, for n = 2,6. Azetidine and pyrrolidine contain chains propagating along 21 screw axes, in which the molecules are linked by co-operative N,H...N hydrogen bonds. Azetidine has two molecules in its asymmetric unit, while pyrrolidine has only one. Hexamethyleneimine contains tetrameric hydrogen-bonded rings formed about crystallographic inversion centres, with two molecules in its asymmetric unit. The observation of crystallographically distinct molecules in the hydrogen-bonded chains of azetidine and cyclic hydrogen-bonded motifs in hexamethyleneimine is consistent with expectations derived from comparison with monoalcohols forming chains or rings by co-operative O,H...O hydrogen bonds. The next member of the cyclic amine series, heptamethyleneimine, forms a cubic plastic phase on cooling from the melt. [source] Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromoleculesACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Paul D. Adams X-ray and neutron crystallographic techniques provide complementary information on the structure and function of biological macromolecules. X-ray and neutron (XN) crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing. The XN approach for complete (including hydrogen) macromolecular structure analysis provides more accurate and complete structures, as demonstrated for diisopropyl fluorophosphatase, photoactive yellow protein and human aldose reductase. Furthermore, this method has several practical advantages, including the easier determination of the orientation of water molecules, hydroxyl groups and some amino-acid side chains. [source] Structure of rat odorant-binding protein OBP1 at 1.6,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2009Scott A. White The nasal mucosa is a specialist interfacial region sandwiched between the olfactory system and the gaseous chemical milieu. In mammals and insects, this region is rich in odorant-binding proteins that are thought to aid olfaction by assisting mass transfer of the many different organoleptic compounds that make up the olfactory landscape. However, in mammals at least, our grasp on the exact function of odorant-binding proteins is tentative and better insight into the role of these proteins is warranted, not least because of their apparent significance in the olfactory systems of insects. Here, the crystal structure of rat odorant-binding protein 1 is reported at 1.6,Å resolution. This protein is one of the best-characterized mammalian odorant-binding proteins and only the third such protein structure to be solved at high resolution. The protein was crystallized in the holo form and contains an unidentifiable ligand that is probably an artefact from the Pichia pastoris expression system. Comparisons are made between this structure and a modelled OBP1 structure produced using the crystal structure of aphrodisin as a template. Comparisons are also made between OBP1 and the other two rat OBP subtypes, for which crystallographic data are unavailable. Interestingly, we also show that OBP1 is monomeric, which is in contrast to its previous assignment. [source] Model-building strategies for low-resolution X-ray crystallographic dataACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Anjum M. Karmali The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5,Å is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered. [source] Structures of and interactions between domains of trigger factor from Thermotoga maritimaACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2007Erik Martinez-Hackert Trigger factor (TF) is a eubacterial chaperone that associates with ribosomes at the peptide-exit tunnel and also occurs in excess free in the cytosol. TF is a three-domain protein that appears to exist in a dynamic equilibrium of oligomerization states and interdomain conformations. X-ray crystallography and chemical cross-linking were used to study the roles of the N- and C-terminal domains of Thermotoga maritima TF in TF oligomerization and chaperone activity. The structural conservation of both the N- and C-terminal TF domains was unambiguously established. The biochemical and crystallographic data reveal a tendency for these domains to partake in diverse and apparently nonspecific protein,protein interactions. It is found that the T. maritima and Escherichia coli TF surfaces lack evident exposed hydrophobic patches. Taken together, these data suggest that TF chaperones could interact with nascent proteins via hydrophilic surfaces. [source] A molecular viewer for the analysis of TLS rigid-body motion in macromoleculesACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005Jay Painter TLS (translation/libration/screw) models describe rigid-body vibrational motions of arbitrary objects. A single-group TLS model can be used to approximate the vibration of an entire protein molecule within a crystal lattice. More complex TLS models are broadly applicable to describing inter-domain and other internal vibrational modes of proteins. Such models can be derived and refined from crystallographic data, but they can also be used to describe the vibrational modes observed through other physical techniques or derived from molecular dynamics. The use of TLS models for protein motion has been relatively limited, partly because the physical meaning of the refined TLS parameters is not intuitive. Here, a molecular viewer, TLSView, is introduced using OpenGL and based on the mmLib library for describing and manipulating macromolecular structural models. This visualization tool allows an intuitive understanding of the physical significance of TLS models derived from crystallographic or other data and may be used as an interactive tool to display and interpret inter-domain or other motions in protein structural models. TLSView may also be used to prepare, analyze and validate TLS models for crystallographic refinement. [source] Structure of DsbC from Haemophilus influenzaeACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2004Man Zhang Bacterial DsbC proteins are involved in rearranging or reducing mismatched disulfide bonds folding within the periplasm. The X-ray structure of the enzyme from Haemophilus influenzae has been solved and compared with the known structure of the Escherichia coli protein. The proteins act as V-shaped dimers with a large cleft to accommodate substrate proteins. The dimers are anchored by a small N-terminal domain, but have a flexible linker region which allows the larger C-terminal domain, with its reactive sulfhydryls, to clamp down on substrates. The overall folds are very similar, but the comparison shows a wider range of hinge motions than previously thought. The crystal packing of the H. influenzae protein allows the movement of the N-terminal domain with respect to the C-terminal domain through motions in the flexible hinge, generating high thermal parameters and unusually high anisotropy in the crystallographic data. [source] Crystallization and preliminary crystallographic data of a leucotoxin S component from Staphylococcus aureusACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2004Valérie Guillet Class S proteins of staphylococcal bicomponent pore-forming leucotoxins play an important role in membrane targetting and cell specificity. Wild-type and recombinant S components of the Panton,Valentine leucocidin (LukS-PV) were expressed in Staphylococcus aureus and Escherichia coli, respectively, and purified. Both proteins were crystallized in two crystal forms with Jeffamine M-600 as the precipitant at 285,K using the hanging-drop vapour-diffusion method and seeding techniques. Crystals belong to space group P2 (or P21) and P41 (or P43), with unit-cell parameters a = 72.3, b = 95.1, c = 108.1,Å, , = 106.4° and a = b = 94.8, c = 306.2,Å, respectively. A full set of X-ray diffraction data was collected to 2.1,Å from a single tetragonal crystal of the wild-type protein at 100,K. [source] Two polymorphs of lysozyme nitrate: temperature dependence of their solubilityACTA CRYSTALLOGRAPHICA SECTION D, Issue 10-1 2002L. Legrand Two crystallographic forms of lysozyme nitrate are known, namely monoclinic and triclinic. Having previously determined the temperature dependence of the solubility of the monoclinic form (0.2 M NaNO3 solutions at pH = 4.5) [Legrand et al. (2001). J. Crystal Growth232, 244-249], we focus here on the solubility of the triclinic form. The temperature dependence of the solubility of this crystallographic form has been measured with a static light device developed in our laboratory. This device allows to observe of the dissolution of one phase and/or the occurrence of a new one by varying the temperature with a sweep rate as low as 0.6 degree/hour. The new solubility data are complemented with crystallographic data of the triclinic form for the sake of completeness. The faces of a triclinic crystal are indexed. The crystallisation enthalpy of the triclinic form is deduced from these new results. These new solubility data allow us now to discuss (1) the publishedprotocols used to obtain the monoclinic and triclinic forms of lysozyme nitrate and (2) the phase transformation. [source] Life-science applications of the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 6-1 2002Robin Taylor Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling of in vivo situations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary to in vacuo theoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein,ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding `hot spots' on proteins, docking ligands into enzyme active sites, de novo ligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules. [source] How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic dataACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2001Boguslaw Stec Contrary to the expectation of chemists, the first X-ray structures of carbon monoxide bound to myoglobin (Mb) showed a highly distorted Fe,C,O bond system. These results appeared to support the idea of a largely steric mechanism for discrimination by the protein against CO binding, a lethal act for the protein in terms of its physiological function. The most recent independently determined high-resolution structures of Mb,CO have allowed the 25,year old controversy concerning the mode of CO binding to be resolved. The CO is now seen to bind in a roughly linear fashion without substantial bending, consistent with chemical expectations and spectroscopic measurements. Access to deposited diffraction data prompted a reevaluation of the sources of the original misinterpretation. A series of careful refinements of models against the data at high (1.1,Å) and modest resolutions (1.5,Å) have been performed in anisotropic versus isotropic modes. The results suggest that the original artifact was a result of lower quality crystals combined with anisotropic motion and limited resolution of the diffraction data sets. This retrospective analysis should serve as a caution for all researchers using structural tools to draw far-reaching biochemical conclusions. [source] Validation of protein crystal structuresACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2000Gerard J. Kleywegt Since the process of building and refining a model of a biomacromolecule based on crystallographic data is subjective, quality-control techniques are required to assess the validity of such models. During the 1990s, much experience was gained; the methods used and some of the lessons learned are reviewed here. In addition, an extensive compendium of quality criteria and quality-control methods that are or have been used to validate models of biomacromolecules has been compiled. The emphasis in this compendium is on the validation of protein crystal structures. [source] Expression, purification, crystallization and preliminary X-ray crystallographic data from TktA, a transketolase from the lactic acid bacterium Lactobacillus salivariusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Matt Horsham The enzyme transketolase from the lactic acid bacterium Lactobacillus salivarius (subsp. salivarius UCC118) has been recombinantly expressed and purified using an Escherichia coli expression system. Purified transketolase from L. salivarius has been crystallized using the vapour-diffusion technique. The crystals belonged to the trigonal space group P3221, with unit-cell parameters a = b = 75.43, c = 184.11,Å, and showed diffraction to 2.3,Å resolution. [source] | |||||||||||||||||||||||||||||||