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Anomalous Dispersion (anomalous + dispersion)
Kinds of Anomalous Dispersion Terms modified by Anomalous Dispersion Selected AbstractsAnomalous Dispersion in Predictive RenderingCOMPUTER GRAPHICS FORUM, Issue 4 2009Andrea Weidlich Abstract In coloured media, the index of refraction does not decrease monotonically with increasing wavelength, but behaves in a quite non-monotonical way. This behaviour is called anomalous dispersion and results from the fact that the absorption of a material influences its index of refraction. So far, this interesting fact has not been widely acknowledged by the graphics community. In this paper, we demonstrate how to calculate the correct refractive index for a material based on its absorption spectrum with the Kramers-Kronig relation, and we discuss for which types of objects this effect is relevant in practice. [source] Iron K -edge anomalous small-angle X-ray scattering at 15-ID-D at the Advanced Photon SourceJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2007Nigel Kirby Small-angle X-ray scattering (SAXS) is an ideal technique for characterizing inorganic nanoparticles in biological specimens large enough to be representative of tissues. As tissues consist of complex mixtures of structures, identifying particular structural features from single-wavelength scattering data can be problematic. Synchrotron SAXS can supply element-specific structural information in complex samples, using anomalous scattering close to absorption edges. Anomalous dispersion is a secondary effect that produces relatively subtle changes in scattering patterns. In order to utilize this effect for anomalous SAXS analysis, stringent control of instrument performance is required. This work outlines the development of high-quality data collection and processing strategies for Fe K -edge anomalous SAXS on the ChemMatCARS beamline at the Advanced Photon Source (APS), Chicago, with an emphasis on intensity normalization. The methods reported here were developed during a study of iron-loaded mammal tissues, but could equally well be applied to other complex specimens. [source] Anomalous Dispersion in Predictive RenderingCOMPUTER GRAPHICS FORUM, Issue 4 2009Andrea Weidlich Abstract In coloured media, the index of refraction does not decrease monotonically with increasing wavelength, but behaves in a quite non-monotonical way. This behaviour is called anomalous dispersion and results from the fact that the absorption of a material influences its index of refraction. So far, this interesting fact has not been widely acknowledged by the graphics community. In this paper, we demonstrate how to calculate the correct refractive index for a material based on its absorption spectrum with the Kramers-Kronig relation, and we discuss for which types of objects this effect is relevant in practice. [source] Polarization switching in BaTiO3 thin films measured by X-ray diffraction exploiting anomalous dispersionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2004S. J. Van Reeuwijk Films of BaTiO3 ranging from 20,nm to 300,nm in thickness were grown with pulsed laser deposition on Nb:SrTiO3. The quality of the layers was investigated using atomic force microscopy, X-ray reflectivity and X-ray diffraction. Both the micrographs and the X-ray reflectivity spectra indicate a smooth surface of the layers. The X-ray diffraction profiles measured using synchrotron radiation show features characteristic for highly crystalline thin films. The application of an external electric field parallel to the c axis changes an hkl reflection of BaTiO3 to an hk reflection. Due to the anomalous dispersion, the intensities of these two reflections are not equal and the atomic displacements can be determined from the intensity differences. The electric field-induced intensity changes can be as large as a few percent, which makes data collection from a 100,nm film using Cu K, radiation from an X-ray tube feasible. The ,I/I values of a number of reflections from the 20 and 50,nm films were measured using synchrotron radiation. The observed ,I/I values were in good agreement with the intensity changes expected for polarization switching in the bulk. [source] Clear strategy screens for macromolecular crystallizationJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2001Andrzej Marek Brzozowski The development of high-throughput crystallography combined with the wealth of already accumulated information about protein crystallization properties requires constant revision of current crystallization screening procedures. Two complementary 6 × 4 matrix `clear strategy screens' (CSS) have been developed and tested on a number of previously non-crystallized proteins. The screens yielded diffraction-quality crystals of a wide range of proteins (enzymes, transcription factors, structural proteins, etc.) in cases where the applications of commercially available screens were unsuccessful. Both their inherently simple design and their flexible nature provide an experimenter with a logical platform for further modification and optimization. Furthermore, the screens facilitate cryoprotection and potential incorporation of anomalous scatterers for multiple/single-wavelength anomalous dispersion (MAD/SAD) experiments. [source] MAD techniques applied to powder data: finding the structure given the substructureACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2009Angela Altomare The joint probability distribution function method is applied to multiple-wavelength anomalous dispersion (MAD) powder data. The distributions are calculated by assuming prior knowledge of the scattering intensities at two wavelengths and of the anomalous-scatterer substructure. The method leads to formulas estimating the full structure phases and their reliability. The procedure has been applied to two structures, one unknown and one known; the second was used as a control for the phasing procedure. In spite of the unavoidable peak overlapping in the diffraction pattern, the formulas proved to be very effective. Combined with a new algorithm for phase extension, they enabled the solution of both crystal structures. [source] Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Å resolutionPROTEIN SCIENCE, Issue 7 2005Ryoichi Arai Abstract The enhancer of rudimentary gene, e(r), of Drosophila melanogaster encodes an enhancer of rudimentary (ER) protein with functions implicated in pyrimidine biosynthesis and the cell cycle. The ER homolog (ERH) is highly conserved among vertebrates, invertebrates, and plants. Xenopus laevis ERH was reported to be a transcriptional repressor. Here we report the 2.1 Å crystal structure of murine ERH (Protein Data Bank ID 1WZ7), determined by the multiwavelength anomalous dispersion (MAD) method. The monomeric structure of ERH comprises a single domain consisting of three ,-helices and four ,-strands, which is a novel fold. In the crystal structure, ERH assumes a dimeric structure, through interactions between the ,-sheet regions. The formation of an ERH dimer is consistent with the results of analytical ultracentrifugation. The residues at the core region and at the dimer interface are highly conserved, suggesting the conservation of the dimer formation as well as the monomer fold. The long flexible loop (44,53) is also significantly conserved, suggesting that this loop region may be important for the functions of ERH. In addition, the putative phosphorylation sites are located at the start of the ,2-strand (Thr18) and at the start of the ,1-helix (Ser24), implying that the phosphorylation might cause some structural changes. [source] All three Ca2+ -binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelinPROTEIN SCIENCE, Issue 3 2005Lu Deng HLH, helix,loop,helix; HSQC, heteronuclear single quantum coherence; RMSD, root mean square deviation; SAD, single wavelength anomalous dispersion Abstract The crystal structures of calcium-loaded apoaequorin and apo-obelin have been determined at resolutions 1.7 Å and 2.2 Å, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-proteins retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hydroperoxycoelenterazine, and also the same as the Ca2+ -discharged obelin bound with the product, coelenteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these subtle shifts are the basis of the ability of these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed. [source] Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8PROTEIN SCIENCE, Issue 11 2004Mutsuko Kukimoto-Niino Abstract TT1887 and TT1465 from Thermus thermophilus HB8 are conserved hypothetical proteins, and are annotated as possible lysine decarboxylases in the Pfam database. Here we report the crystal structures of TT1887 and TT1465 at 1.8 Å and 2.2 Å resolutions, respectively, as determined by the multiwavelength anomalous dispersion (MAD) method. TT1887 is a homotetramer, while TT1465 is a homohexamer in the crystal and in solution. The structures of the TT1887 and TT1465 monomers contain single domains with the Rossmann fold, comprising six , helices and seven , strands, and are quite similar to each other. The major structural differences exist in the N terminus of TT1465, where there are two additional , helices. A comparison of the structures revealed the elements that are responsible for the different oligomerization modes. The distributions of the electrostatic potential on the solvent-accessible surfaces suggested putative active sites. [source] Crystal structure of E. coli ,,carbonic anhydrase, an enzyme with an unusual pH,dependent activityPROTEIN SCIENCE, Issue 5 2001Jeff D. Cronk CA, carbonic anhydrase; ECCA, Escherichia coli ,-carbonic anhydrase; PPCA, Porphyridium purpureum ,-carbonic anhydrase; PSCA, Pisum sativum ,-carbonic anhydrase; EXAFS, extended X-ray absorption fine structure spectroscopy; MAD, multiwavelength anomalous dispersion Abstract Carbonic anhydrases fall into three distinct evolutionary and structural classes: ,, ,, and ,. The ,-class carbonic anhydrases (,-CAs) are widely distributed among higher plants, simple eukaryotes, eubacteria, and archaea. We have determined the crystal structure of ECCA, a ,-CA from Escherichia coli, to a resolution of 2.0 Å. In agreement with the structure of the ,-CA from the chloroplast of the red alga Porphyridium purpureum, the active-site zinc in ECCA is tetrahedrally coordinated by the side chains of four conserved residues. These results confirm the observation of a unique pattern of zinc ligation in at least some ,-CAs. The absence of a water molecule in the inner coordination sphere is inconsistent with known mechanisms of CA activity. ECCA activity is highly pH-dependent in the physiological range, and its expression in yeast complements an oxygen-sensitive phenotype displayed by a ,-CA-deletion strain. The structural and biochemical characterizations of ECCA presented here and the comparisons with other ,-CA structures suggest that ECCA can adopt two distinct conformations displaying widely divergent catalytic rates. [source] The magic triangle goes MAD: experimental phasing with a bromine derivativeACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Tobias Beck Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br,K edge was successfully carried out. Radiation damage to the bromine,carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out. [source] Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxinACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Megan Guelker The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3121 and P43, at 2.5 and 2.0,Å resolution, respectively. Structure determination in space group P3121 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3121 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P43, which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3121 crystal form. During the early stages of refinement, application of the appropriate twin law, (,h, ,k, l), was required to converge to reasonable R -factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition. [source] Structure of a fatty acid-binding protein from Bacillus subtilis determined by sulfur-SAD phasing using in-house chromium radiationACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2009Jie Nan Sulfur single-wavelength anomalous dispersion (S-SAD) and halide-soaking methods are increasingly being used for ab initio phasing. With the introduction of in-house Cr X-ray sources, these methods benefit from the enhanced anomalous scattering of S and halide atoms, respectively. Here, these methods were combined to determine the crystal structure of BsDegV, a DegV protein-family member from Bacillus subtilis. The protein was cocrystallized with bromide and low-redundancy data were collected to 2.5,Å resolution using Cr,K, radiation. 17 heavy-atom sites (ten sulfurs and seven bromides) were located using standard methods. The anomalous scattering of some of the BsDegV S atoms and Br atoms was weak, thus neither sulfurs nor bromides could be used alone for structure determination using the collected data. When all 17 heavy-atom sites were used for SAD phasing, an easily interpretable electron-density map was obtained after density modification. The model of BsDegV was built automatically and a palmitate was found tightly bound in the active site. Sequence alignment and comparisons with other known DegV structures provided further insight into the specificity of fatty-acid selection and recognition within this protein family. [source] Crystallization of a pentapeptide-repeat protein by reductive cyclic pentylation of free amines with glutaraldehydeACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2009Matthew W. Vetting The pentapeptide-repeat protein EfsQnr from Enterococcus faecalis protects DNA gyrase from inhibition by fluoroquinolones. EfsQnr was cloned and purified to homogeneity, but failed to produce diffraction-quality crystals in initial crystallization screens. Treatment of EfsQnr with glutaraldehyde and the strong reducing agent borane,dimethylamine resulted in a derivatized protein which produced crystals that diffracted to 1.6,Å resolution; their structure was subsequently determined by single-wavelength anomalous dispersion. Analysis of the derivatized protein using Fourier transform ion cyclotron resonance mass spectrometry indicated a mass increase of 68,Da per free amino group. Electron-density maps about a limited number of structurally ordered lysines indicated that the modification was a cyclic pentylation of free amines, producing piperidine groups. [source] Structure analysis of the conserved methyltransferase domain of human trimethylguanosine synthase TGS1ACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2009Thomas Monecke Methyltransferases play an important role in the post-transcriptional maturation of most ribonucleic acids. The modification of spliceosomal UsnRNAs includes N2-dimethylation of the m7G cap catalyzed by trimethylguanosine synthase 1 (TGS1). This 5,-cap hypermethylation occurs during the biogenesis of UsnRNPs as it initiates the m3G cap-dependent nuclear import of UsnRNPs. The conserved methyltransferase domain of human TGS1 has been purified, crystallized and the crystal structure of this domain with bound substrate m7GpppA was solved by means of multiple-wavelength anomalous dispersion. Crystal structure analysis revealed that m7GpppA binds via its adenosine moiety to the structurally conserved adenosylmethionine-binding pocket, while the m7 guanosine remains unbound. This unexpected binding only occurs in the absence of AdoMet and suggests an incomplete binding pocket for the m7G cap which is caused by the N-terminal truncation of the protein. These structural data are consistent with the finding that the crystallized fragment of human TGS1 is catalytically inactive, while a fragment that is 17 amino acids longer exhibits activity. [source] Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2006Luke A. Moe The structure of the Rieske-type ferredoxin (T4moC) from toluene 4-monooxygenase was determined by X-ray crystallography in the [2Fe,2S]2+ state at a resolution of 1.48,Å using single-wavelength anomalous dispersion phasing with the [2Fe,2S] center. The structure consists of ten ,-strands arranged into the three antiparallel ,-sheet topology observed in all Rieske proteins. Trp69 of T4moC is adjacent to the [2Fe,2S] centre, which displaces a loop containing the conserved Pro81 by ,8,Å away from the [2Fe,2S] cluster compared with the Pro loop in the closest structural and functional homolog, the Rieske-type ferredoxin BphF from biphenyl dioxygenase. In addition, T4moC contains five hydrogen bonds to the [2Fe,2S] cluster compared with three hydrogen bonds in BphF. Moreover, the electrostatic surface of T4moC is distinct from that of BphF. These structural differences are identified as possible contributors to the evolutionary specialization of soluble Rieske-type ferredoxins between the diiron monooxygenases and cis -dihydrodiol-forming dioxygenases. [source] Crystallization of FLINC4, an intramolecular LMO4,ldb1 complexACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2003Janet E. Deane LMO4 is the most recently discovered member of a small family of nuclear transcriptional regulators that are important for both normal development and disease processes. LMO4 is comprised primarily of two tandemly repeated LIM domains and interacts with the ubiquitous nuclear adaptor protein ldb1. This interaction is mediated via the LIM domains of LMO4 and the LIM-interaction domain (LID) of ldb1. An intramolecular complex, termed FLINC4, consisting of the two LIM domains from LMO4 linked to the LID domain of ldb1 via a flexible linker has been engineered, purified and crystallized. The trigonal crystals, which belong to space group P312 with unit-cell parameters a = 61.3, c = 93.2,Å, diffract to 1.3,Å resolution and contain one molecule of FLINC4 per asymmetric unit. Native and multiple-wavelength anomalous dispersion (MAD) data collected at the Zn X-ray absorption edge have been recorded to 1.3 and 1.7,Å resolution, respectively. Anomalous Patterson maps calculated with data collected at the peak wavelength show strong peaks sufficient to determine the positions of four Zn atoms per asymmetric unit. [source] High-resolution structure of human phosphoserine phosphatase in open conformationACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2003Yves Peeraer The crystal structure of human phosphoserine phosphatase (HPSP) in the open conformation has been determined at a resolution of 1.53,Å. The crystals are orthorhombic, belonging to space group C2221, with unit-cell parameters a = 49.03, b = 130.25, c = 157.29,Å. The asymmetric unit contains two molecules. Phase information was derived from a multiwavelength anomalous dispersion (MAD) experiment conducted at three wavelengths using a selenomethionine-derivative crystal of HPSP. The structure was refined using CNS to a final crystallographic R value of 21.6% (Rfree = 23.4%). HPSP is a dimeric enzyme responsible for the third and final step of the l -serine biosynthesis pathway. It catalyses the Mg2+ -dependent hydrolysis of l -phosphoserine. Recently, the structure of HPSP in complex with an inhibitor bound to the active site has been reported to be the open conformation of the enzyme. Here, the structure of HPSP is reported in the absence of substrate in the active site. Evidence is presented that HPSP in an uncomplexed form is in an even more open conformation than in the inhibitor complex. In this state, the enzyme is partially unfolded to allow the substrate to enter the active site. Binding of the substrate causes HPSP to shift to the closed conformation by stabilizing the partially unfolded region. In the present structure a Ca2+ ion is bound to the active site and an explanation is given why HPSP is not active when in the active site Mg2+ is replaced by a Ca2+ ion. [source] Phasing power at the K absorption edge of organic arsenicACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2003Pascal Retailleau Single/multiple-wavelength anomalous dispersion (SAD/MAD) experiments were performed on a crystal of an organic arsenic derivative of hen egg-white lysozyme. A para -arsanilate compound used as a crystallizing reagent was incorporated into the ordered solvent region of the lysozyme molecule. Diffraction data were collected to high resolution (,2.0,Å) at three wavelengths around the K edge (1.04,Å) of arsenic at beamline BM30A, ESRF synchrotron. Anomalous Patterson maps clearly showed the main arsanilate site to be between three symmetry-related lysozyme molecules, at a location previously occupied by a para -toluenesulfonate anion. MAD phases at 2,Å derived using the program SHARP led to an electron-density map of sufficient quality to start manual building of the protein model. Amplitudes from a second crystal measured to a resolution of 1.8,Å at the peak wavelength revealed two additional heavy-atom sites, which reinforced the anomalous subset model and therefore dramatically improved the phasing power of the arsenic derivative. The subsequent solvent-flattened map was of such high accuracy that the program ARP/wARP was able to build a nearly complete model automatically. This work emphasizes the great potential of arsenic for de novo structure determination using anomalous dispersion methods. [source] X-ray-induced debromination of nucleic acids at the Br,K absorption edge and implications for MAD phasingACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2002E. Ennifar Multi-wavelength anomalous dispersion (MAD) using brominated derivatives is considered a common and convenient technique for solving chemically synthesized nucleic acid structures. Here, it is shown that a relatively moderate X-ray dose (of the order of 5 × 1015,photons,mm,2) can induce sufficient debromination to prevent structure determination. The decrease in bromine occupancy with radiation dose can be accounted for by a simple exponential, with an estimated rate constant at the absorption-peak wavelength, 7.4,(0.8),MGy, that is not significantly different from its value at the absorption-edge wavelength, 9.2,(2.6),MGy (the given e.s.d.s assess the relative closeness of the two values, not their absolute accuracy, which is probably worse). Chemically, these results (and others) are consistent with bromine cleavage resulting from direct photodissociation and/or from the action of free electrons, rather than from the action of hydroxyl radicals originating from water dissociation. The free bromine species (Br,) diffuse too quickly, even in amorphous ice around 100,K, to allow the determination of a diffusion coefficient. From a practical point of view, it is suggested that a single data collection with a crystal consisting of iodinated instead of brominated derivatives could provide both anomalous scattering and SIR phase information by the progressive cleavage of iodine. [source] 3-Carboxy- cis,cis -muconate lactonizing enzyme from Neurospora crassa: MAD phasing with 80 selenomethioninesACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2002Michael C. Merckel The structure of 3-carboxy- cis,cis -muconate lactonizing enzyme from Neurospora crassa was determined at 3.0,Å resolution. Phase information was derived from a multiwavelength anomalous dispersion (MAD) experiment conducted at three wavelengths using crystals of fully substituted selenomethionine protein. However, the structure determination was not routine owing to the relatively poor quality of the diffraction data and the large number of twofolds in the unit cell. Eventually, 80 selenium sites were identified by the combined use of direct methods and real-space map interpretation. This represents one of the largest selenium substructures solved and used for phasing. Some of the difficulties in the structure determination and the methods used to address them are discussed. [source] Gd-HPDO3A, a complex to obtain high-phasing-power heavy-atom derivatives for SAD and MAD experiments: results with tetragonal hen egg-white lysozymeACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2002Éric Girard A neutral gadolinium complex, Gd-HPDO3A, is shown to be a good candidate to use to obtain heavy-atom derivatives and solve macromolecular structures using anomalous dispersion. Tetragonal crystals of a gadolinium derivative of hen egg-white lysozyme were obtained by co-crystallization using different concentrations of the complex. Diffraction data from three derivative crystals (100, 50 and 10,mM) were collected to a resolution of 1.7,Å using Cu,K, radiation from a rotating anode. Two strong binding sites of the gadolinium complex to the protein were located from the gadolinium anomalous signal in both the 100 and 50,mM derivatives. A single site is occupied in the 10,mM derivative. Phasing using the anomalous signal at a single wavelength (SAD method) leads to an electron-density map of high quality. The structure of the 100,mM derivative has been refined. Two molecules of the gadolinium complex are close together. Both molecules are located close to tryptophan residues. Four chloride ions were found. The exceptional quality of the SAD electron-density map, only enhanced by solvent flattening, suggests that single-wavelength anomalous scattering with the Gd-HPDO3A complex may be sufficient to solve protein structures of high molecular weight by synchrotron-radiation experiments, if not by laboratory experiments. [source] Novel approach to phasing proteins: derivatization by short cryo-soaking with halidesACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2000Zbigniew Dauter A quick (less than 1,min) soak of protein crystals in a cryo-solution containing bromide or iodide anions leads to incorporation of these anomalous scatterers into the ordered solvent region around the protein molecules. These halide anions provide a convenient way of phasing through their anomalous scattering signal: bromides using multiwavelength anomalous dispersion (MAD) and bromides and/or iodides using single-wavelength anomalous dispersion (SAD) or single isomorphous replacement with anomalous scattering (SIRAS) methods. This approach has been tested successfully on four different proteins and has been used to solve the structure of a new protein of molecular weight 30,kDa. [source] Structure of Stenotrophomonas maltophilia FeoA complexed with zinc: a unique prokaryotic SH3-domain protein that possibly acts as a bacterial ferrous iron-transport activating factorACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010Yi-Che Su Iron is vital to the majority of prokaryotes, with ferrous iron believed to be the preferred form for iron uptake owing to its much better solubility. The major route for bacterial ferrous iron uptake is found to be via an Feo (ferrous iron-transport) system comprising the three proteins FeoA, FeoB and FeoC. Although the structure and function of FeoB have received much attention recently, the roles played by FeoA and FeoC have been little investigated to date. Here, the tertiary structure of FeoA from Stenotrophomonas maltophilia (Sm), a vital opportunistic pathogen in immunodepressed hosts, is reported. The crystal structure of SmFeoA has been determined to a resolution of 1.7,Å using an Se single-wavelength anomalous dispersion (Se-SAD) approach. Although SmFeoA bears low sequence identity to eukaryotic proteins, its structure is found to adopt a eukaryotic SH3-domain-like fold. It also bears weak similarity to the C-terminal SH3 domain of bacterial DtxR (diphtheria toxin regulator), with some unique characteristics. Intriguingly, SmFeoA is found to adopt a unique dimer cross-linked by two zinc ions and six anions (chloride ions). Since FeoB has been found to contain a G-protein-like domain with low GTPase activity, FeoA may interact with FeoB through the SH3,G-protein domain interaction to act as a ferrous iron-transport activating factor. [source] Purification, crystallization and preliminary X-ray analysis of human GIMAP2ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010David Schwefel GTPases of immunity-associated proteins (GIMAPs) are important regulators of T-cell death and survival. Here, the crystallization and data collection of three GIMAP2 constructs in various nucleotide-loaded states is described. Selenomethionine-substituted carboxy-terminally truncated GIMAP2 (amino-acid residues 1,260; GIMAP21,260) in the nucleotide-free form crystallized in space group P212121 and the crystals diffracted X-rays to 1.5,Å resolution. The phase problem was solved using the single anomalous dispersion (SAD) protocol. GDP-bound GIMAP221,260 and GDP-bound GIMAP21,234 crystallized in space group P212121 and the crystals diffracted X-rays to 2.9 and 1.7,Å resolution, respectively. GTP-bound GIMAP21,234 crystallized in space group C2221 and the crystals diffracted to 1.9,Å resolution. These results will allow a detailed structural analysis of GIMAP2, which will provide insight into the architecture and function of the GIMAP family. [source] Crystallization and X-ray analysis of human cytoplasmic phenylalanyl-tRNA synthetaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009Igal Finarov Human cytosolic phenylalanyl-tRNA synthetase (hcPheRS) is responsible for the covalent attachment of phenylalanine to its cognate tRNAPhe. Significant differences between the amino-acid sequences of eukaryotic and prokaryotic PheRSs indicate that the domain composition of hcPheRS differs from that of the Thermus thermophilus analogue. As a consequence of the absence of the anticodon-recognizing B8 domain, the binding mode of tRNAPhe to hcPheRS is expected to differ from that in prokaryotes. Recombinant hcPheRS protein was purified to homogeneity and crystallized. The crystals used for structure determination diffracted to 3.3,Å resolution and belonged to space group C2, with unit-cell parameters a = 362.9, b = 213.6, c = 212.7,Å, , = 125.2°. The structure of hcPheRS was determined by the molecular-replacement method in combination with phase information from multiwavelength anomalous dispersion. [source] Overexpression, purification, characterization and preliminary crystallographic study of phosphoglycolate phosphatase from Shigella flexneri 2a strain 301ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2009Heli Liu Phosphoglycolate phosphatase has a salvage function in the metabolism of the 2-phosphoglycolate formed during bacterial DNA repair. In order to better understand its dimerization behaviour, the influence of metal ions on its activity and its catalytic mechanism at the molecular level, recombinant phosphoglycolate phosphatase from Shigella flexneri was overexpressed, purified, characterized and crystallized by the hanging-drop vapour-diffusion method at 291,K using polyethylene glycol 3500 as a precipitant and zinc acetate as an additive. The crystals belonged to space group R3, with unit-cell parameters a = 88.1, b = 88.1, c = 259.2,Å, corresponding to the presence of two molecules in the asymmetric unit. SeMet-labelled protein was also prepared and crystallized for use in phase determination. Initial structure determination using the multiwavelength anomalous dispersion (MAD) method clearly revealed that SfPGPase bears an ,-helical cap domain that differs from that of a previously reported orthologue. [source] Rv0802c from Mycobacterium tuberculosis: the first structure of a succinyltransferase with the GNAT foldACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2008Matthew W. Vetting Gene rv0802c from Mycobacterium tuberculosis encodes a 218-amino-acid protein and is annotated as a hypothetical protein with homology to GCN5-related N -acetyltransferases. The structure of Rv0802c was determined in an unliganded form to 2.0,Å resolution utilizing single-wavelength anomalous dispersion from a samarium soak that resulted in a single bound Sm3+:citrate2 complex. The structure confirms that Rv0802c exhibits the GCN5-related N -acetyltransferase fold and revealed a tetramer composed of a dimer of dimers with approximate 222 symmetry. In addition, a bound acetate ion indicated that Rv0802c may utilize a unique acyl donor for the family. The subsequent determination of the structure of Rv0802c in complex with succinyl-CoA to 2.3,Å resolution suggests that Rv0802c is the first known GCN5-related N -acetyltransferase family member to utilize succinyl-CoA as a substrate. [source] Expression, crystallization and preliminary crystallographic studies of a novel bifunctional N -acetylglutamate synthase/kinase from Xanthomonas campestris homologous to vertebrate N -acetylglutamate synthaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2006Dashuang Shi A novel N -acetylglutamate synthase/kinase bifunctional enzyme of arginine biosynthesis that was homologous to vertebrate N -acetylglutamate synthases was identified in Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the hexagonal space group P6222, with unit-cell parameters a = b = 134.60, c = 192.11,Å, and diffract to about 3.0,Å resolution. Selenomethionine-substituted recombinant protein was produced and selenomethionine substitution was verified by mass spectroscopy. Multiple anomalous dispersion (MAD) data were collected at three wavelengths at SER-CAT, Advanced Photon Source, Argonne National Laboratory. Structure determination is under way using the MAD phasing method. [source] Structure of the conserved hypothetical protein MAL13P1.257 from Plasmodium falciparumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2006Margaret A. Holmes The structure of a conserved hypothetical protein, PlasmoDB sequence MAL13P1.257 from Plasmodium falciparum, Pfam sequence family PF05907, has been determined as part of the structural genomics effort of the Structural Genomics of Pathogenic Protozoa consortium. The structure was determined by multiple-wavelength anomalous dispersion at 2.17,Å resolution. The structure is almost entirely ,-sheet; it consists of 15 ,-strands and one short 310 -helix and represents a new protein fold. The packing of the two monomers in the asymmetric unit indicates that the biological unit may be a dimer. [source] | ||||||||||