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  • Nature Publishing Group  (42,899)
  • International Union of Crystallography (IUCr)
  • 2000-2004  (19,456)
  • 1980-1984  (23,570)
  • 1925-1929
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  • 1
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    Tropical climate changes at millennial and orbital timescales on the Bolivian Altiplano (2001)
    Nature Publishing Group
    In:  Nature, 409 (6821). pp. 698-701.
    Details
    Publication Date: 2017-01-04
    Description: Tropical South America is one of the three main centres of the global, zonal overturning circulation of the equatorial atmosphere (generally termed the 'Walker' circulation1). Although this area plays a key role in global climate cycles, little is known about South American climate history. Here we describe sediment cores and down-hole logging results of deep drilling in the Salar de Uyuni, on the Bolivian Altiplano, located in the tropical Andes. We demonstrate that during the past 50,000 years the Altiplano underwent important changes in effective moisture at both orbital (20,000-year) and millennial timescales. Long-duration wet periods, such as the Last Glacial Maximum—marked in the drill core by continuous deposition of lacustrine sediments—appear to have occurred in phase with summer insolation maxima produced by the Earth's precessional cycle. Short-duration, millennial events correlate well with North Atlantic cold events, including Heinrich events 1 and 2, as well as the Younger Dryas episode. At both millennial and orbital timescales, cold sea surface temperatures in the high-latitude North Atlantic were coeval with wet conditions in tropical South America, suggesting a common forcing.
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  • 2
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    A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont (2002)
    Nature Publishing Group
    In:  Nature, 417 (6884). pp. 63-67.
    Details
    Publication Date: 2017-07-07
    Description: According to small subunit ribosomal RNA (ss rRNA) sequence comparisons all known Archaea belong to the phyla Crenarchaeota, Euryarchaeota, and—indicated only by environmental DNA sequences—to the 'Korarchaeota'1, 2. Here we report the cultivation of a new nanosized hyperthermophilic archaeon from a submarine hot vent. This archaeon cannot be attached to one of these groups and therefore must represent an unknown phylum which we name 'Nanoarchaeota' and species, which we name 'Nanoarchaeum equitans'. Cells of 'N. equitans' are spherical, and only about 400 nm in diameter. They grow attached to the surface of a specific archaeal host, a new member of the genus Ignicoccus3. The distribution of the 'Nanoarchaeota' is so far unknown. Owing to their unusual ss rRNA sequence, members remained undetectable by commonly used ecological studies based on the polymerase chain reaction4. 'N. equitans' harbours the smallest archaeal genome; it is only 0.5 megabases in size. This organism will provide insight into the evolution of thermophily, of tiny genomes and of interspecies communication.
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  • 3
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    Termination of global warmth at the Palaeocene/Eocene boundary through productivity feedback (2000)
    Nature Publishing Group
    In:  Nature, 407 (6801). pp. 171-174.
    Details
    Publication Date: 2017-01-04
    Description: The onset of the Palaeocene/Eocene thermal maximum (about 55 Myr ago) was marked by global surface temperatures warming by 5–7 °C over approximately 30,000 yr (ref. 1), probably because of enhanced mantle outgassing2, 3 and the pulsed release of approx1,500 gigatonnes of methane carbon from decomposing gas-hydrate reservoirs4, 5, 6, 7. The aftermath of this rapid, intense and global warming event may be the best example in the geological record of the response of the Earth to high atmospheric carbon dioxide concentrations and high temperatures. This response has been suggested to include an intensified flux of organic carbon from the ocean surface to the deep ocean and its subsequent burial through biogeochemical feedback mechanisms8. Here we present firm evidence for this view from two ocean drilling cores, which record the largest accumulation rates of biogenic barium—indicative of export palaeoproductivity—at times of maximum global temperatures and peak excursion values of delta13C. The unusually rapid return of delta13C to values similar to those before the methane release7 and the apparent coupling of the accumulation rates of biogenic barium to temperature, suggests that the enhanced deposition of organic matter to the deep sea may have efficiently cooled this greenhouse climate by the rapid removal of excess carbon dioxide from the atmosphere.
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  • 4
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    Conservation: Biogeography of the Indonesian coelacanths (2000)
    Nature Publishing Group
    In:  Nature, 403 (6765). p. 38.
    Details
    Publication Date: 2017-07-06
    Description: Living coelacanths (Latimeria chalumnae) are normally found only in the western Indian Ocean, where they inhabit submarine caves in the Comores Islands. Two specimens have since been caught off the island of Manado Tua, north Sulawesi, Indonesia, some 10,000 kilometres away. We sought to determine the ecological and geographic distribution of Indonesian coelacanth populations with a view to drawing up conservation measures for this extremely rare fish. During our explorations, we discovered two living Indonesian coelacanths 360 km southwest of Manado Tua.
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  • 5
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    The effects of surfactants on spilling breaking waves (2003)
    Nature Publishing Group
    In:  Nature, 421 (6922). pp. 520-523.
    Details
    Publication Date: 2016-05-10
    Description: Breaking waves markedly increase the rates of air–sea transfer of momentum, energy and mass. In light to moderate wind conditions, spilling breakers with short wavelengths are observed frequently. Theory and laboratory experiments have shown that, as these waves approach breaking in clean water, a ripple pattern that is dominated by surface tension forms at the crest. Under laboratory conditions and in theory, the transition to turbulent flow is triggered by flow separation under the ripples, typically without leading to overturning of the free surface15. Water surfaces in nature, however, are typically contaminated by surfactant films that alter the surface tension and produce surface elasticity and viscosity16, 17. Here we present the results of laboratory experiments in which spilling breaking waves were generated mechanically in water with a range of surfactant concentrations. We find significant changes in the breaking process owing to surfactants. At the highest concentration of surfactants, a small plunging jet issues from the front face of the wave at a point below the wave crest and entraps a pocket of air on impact with the front face of the wave. The bubbles and turbulence created during this process are likely to increase air–sea transfer.
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  • 6
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    Relative departures in July temperatures in northern Canada for the past 6,000 yr (1981)
    Nature Publishing Group
    In:  Nature, 289 (5794). pp. 164-167.
    Details
    Publication Date: 2016-04-11
    Description: There has been concern about recent temperature trends and the future effects of CO2 concentrations in the atmosphere1,2; but instrumental records only cover a few decades to a few centuries and it is essential that proxy data sources, such as pollen spectra from peats and lake sediments, be carefully interpreted as climate records. Several workers have shown statistically significant associations between the modern pollen rain and climatic parameters, an approach that by-passes the recognition of pollen/vegetation units. Statistically defined equations that associate abiotic and biotic elements are called transfer functions. We report here on the application of transfer function equations to nine middle and late Holocene peat and lake sediment sequences from northern Canada (Fig. 1).
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  • 7
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    Particulate organic carbon flux in the oceans-surface productivity and oxygen utilization (1980)
    Nature Publishing Group
    In:  Nature, 288 (5788). pp. 260-263.
    Details
    Publication Date: 2016-03-01
    Description: Organic detritus passing from the sea surface through the water column to the sea floor controls nutrient regeneration, fuels benthic life and affects burial of organic carbon in the sediment record. Particle trap systems have enabled the first quantification of this important process. The results suggest that the dominant mechanism of vertical transport is by rapid settling of rare large particles, most likely of faecal pellets or marine snow of the order of 〉200 μm in diameter, whereas the more frequent small particles have an insignificant role in vertical mass flux4–6. The ultimate source of organic detritus is biological production in surface waters of the oceans. I determine here an empirical relationship that predicts organic carbon flux at any depth in the oceans below the base of the euphotic zone as a function of the mean net primary production rate at the surface and depth-dependent consumption. Such a relationship aids in estimating rates of decay of organic matter in the water column, benthic and water column respiration of oxygen in the deep sea and burial of organic carbon in the sediment record.
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  • 8
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    The ‘zero charge’ partitioning behaviour of noble gases during mantle melting (2003)
    Nature Publishing Group
    In:  Nature, 423 (6941). pp. 738-741.
    Details
    Publication Date: 2015-11-24
    Description: Noble-gas geochemistry is an important tool for understanding planetary processes from accretion to mantle dynamics and atmospheric formation. Central to much of the modelling of such processes is the crystal–melt partitioning of noble gases during mantle melting, magma ascent and near-surface degassing5. Geochemists have traditionally considered the 'inert' noble gases to be extremely incompatible elements, with almost 100 per cent extraction efficiency from the solid phase during melting processes. Previously published experimental data on partitioning between crystalline silicates and melts has, however, suggested that noble gases approach compatible behaviour, and a significant proportion should therefore remain in the mantle during melt extraction. Here we present experimental data to show that noble gases are more incompatible than previously demonstrated, but not necessarily to the extent assumed or required by geochemical models. Independent atomistic computer simulations indicate that noble gases can be considered as species of 'zero charge' incorporated at crystal lattice sites. Together with the lattice strain model9, 10, this provides a theoretical framework with which to model noble-gas geochemistry as a function of residual mantle mineralogy.
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  • 9
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    Genomic islands in pathogenic and environmental microorganisms (2004)
    Nature Publishing Group
    In:  Nature Reviews Microbiology, 2 (5). pp. 414-424.
    Details
    Publication Date: 2020-06-23
    Description: Horizontal gene transfer is an important mechanism for the evolution of microbial genomes. Pathogenicity islands — mobile genetic elements that contribute to rapid changes in virulence potential — are known to have contributed to genome evolution by horizontal gene transfer in many bacterial pathogens. Increasing evidence indicates that equivalent elements in non-pathogenic species — genomic islands — are important in the evolution of these bacteria, influencing traits such as antibiotic resistance, symbiosis and fitness, and adaptation in general. This review discusses the recent lessons that have been learned from pathogenicity islands in pathogenic microorganisms and how they apply to the role of genomic islands in commensal, symbiotic and environmental bacteria.
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  • 10
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    Consumer versus resource control of species diversity and ecosystem functioning (2002)
    Nature Publishing Group
    In:  Nature Geoscience, 417 . pp. 848-851.
    Details
    Publication Date: 2017-02-28
    Description: A key question in ecology is which factors control species diversity in a community1, 2, 3. Two largely separate groups of ecologists have emphasized the importance of productivity or resource supply, and consumers or physical disturbance, respectively. These variables show unimodal relationships with diversity when manipulated in isolation4, 5, 6, 7, 8. Recent multivariate models9, 10, however, predict that these factors interact, such that the disturbance–diversity relationship depends on productivity, and vice versa. We tested these models in marine food webs, using field manipulations of nutrient resources and consumer pressure on rocky shores of contrasting productivity. Here we show that the effects of consumers and nutrients on diversity consistently depend on each other, and that the direction of their effects and peak diversity shift between sites of low and high productivity. Factorial meta-analysis of published experiments confirms these results across widely varying aquatic communities. Furthermore, our experiments demonstrate that these patterns extend to important ecosystem functions such as carbon storage and nitrogen retention. This suggests that human impacts on nutrient supply11 and food-web structure12, 13 have strong and interdependent effects on species diversity and ecosystem functioning, and must therefore be managed together.
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  • 11
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    When the Earth moved: How Earth scientists developed the theory of plate tectonics (2002)
    Nature Publishing Group
    In:  Nature, 417 . pp. 487-488.
    Details
    Publication Date: 2017-03-07
    Description: BOOK REVIEWED: Plate Tectonics: An Insider's History of the Modern Theory of the Earth / edited by Naomi Oreskes Westview Press: 2001. 448 pp.
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  • 12
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    Break-up of the Atlantic Deep Western Boundary Current into eddies at 8°S (2004)
    Nature Publishing Group
    In:  Nature, 432 . pp. 1018-1020.
    Details
    Publication Date: 2017-03-09
    Description: The existence in the ocean of deep western boundary currents, which connect the high-latitude regions where deep water is formed with upwelling regions as part of the global ocean circulation, was postulated more than 40 years ago1. These ocean currents have been found adjacent to the continental slopes of all ocean basins, and have core depths between 1,500 and 4,000 m. In the Atlantic Ocean, the deep western boundary current is estimated to carry (10–40) times 106 m3 s-1 of water2, 3, 4, 5, transporting North Atlantic Deep Water—from the overflow regions between Greenland and Scotland and from the Labrador Sea—into the South Atlantic and the Antarctic circumpolar current. Here we present direct velocity and water mass observations obtained in the period 2000 to 2003, as well as results from a numerical ocean circulation model, showing that the Atlantic deep western boundary current breaks up at 8° S. Southward of this latitude, the transport of North Atlantic Deep Water into the South Atlantic Ocean is accomplished by migrating eddies, rather than by a continuous flow. Our model simulation indicates that the deep western boundary current breaks up into eddies at the present intensity of meridional overturning circulation. For weaker overturning, continuation as a stable, laminar boundary flow seems possible.
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  • 13
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    In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor (2003)
    Nature Publishing Group
    In:  Nature, 424 . pp. 763-765.
    Details
    Publication Date: 2017-03-07
    Description: More than 50% of the Earth' s surface is sea floor below 3,000 m of water. Most of this major reservoir in the global carbon cycle and final repository for anthropogenic wastes is characterized by severe food limitation. Phytodetritus is the major food source for abyssal benthic communities, and a large fraction of the annual food load can arrive in pulses within a few days1, 2. Owing to logistical constraints, the available data concerning the fate of such a pulse are scattered3, 4 and often contradictory5, 6, 7, 8, 9, 10, hampering global carbon modelling and anthropogenic impact assessments. We quantified (over a period of 2.5 to 23 days) the response of an abyssal benthic community to a phytodetritus pulse, on the basis of 11 in situ experiments. Here we report that, in contrast to previous hypotheses5, 6, 7, 8, 9, 10, 11, the sediment community oxygen consumption doubled immediately, and that macrofauna were very important for initial carbon degradation. The retarded response of bacteria and Foraminifera, the restriction of microbial carbon degradation to the sediment surface, and the low total carbon turnover distinguish abyssal from continental-slope ‘deep-sea’ sediments.
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  • 14
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    Paleoceanographic implications of genetic variation in living North Atlantic Neogloboquadrina pachyderma (2003)
    Nature Publishing Group
    In:  Nature, 424 (6946). pp. 299-302.
    Details
    Publication Date: 2017-03-07
    Description: The shells of the planktonic foraminifer Neogloboquadrina pachyderma have become a classical tool for reconstructing glacial–interglacial climate conditions in the North Atlantic Ocean1, 2, 3. Palaeoceanographers utilize its left- and right-coiling variants, which exhibit a distinctive reciprocal temperature and water mass related shift in faunal abundance both at present and in late Quaternary sediments1, 2, 4, 5. Recently discovered cryptic genetic diversity in planktonic foraminifers6, 7, 8 now poses significant questions for these studies. Here we report genetic evidence demonstrating that the apparent ‘single species’ shell-based records of right-coiling N. pachyderma used in palaeoceanographic reconstructions contain an alternation in species as environmental factors change. This is reflected in a species-dependent incremental shift in right-coiling N. pachyderma shell calcite δ18O between the Last Glacial Maximum and full Holocene conditions. Guided by the percentage dextral coiling ratio, our findings enhance the use of δ18O records of right-coiling N. pachyderma for future study. They also highlight the need to genetically investigate other important morphospecies to refine their accuracy and reliability as palaeoceanographic proxies.
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  • 15
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    Palaeoceanography: Antarctic stratification and glacial CO2 (2001)
    Nature Publishing Group
    In:  Nature, 412 . pp. 605-606.
    Details
    Publication Date: 2017-02-28
    Description: One way of accounting for lowered atmospheric carbon dioxide concentrations during Pleistocene glacial periods is by invoking the Antarctic stratification hypothesis, which links the reduction in CO2 to greater stratification of ocean surface waters around Antarctica1, 2. As discussed by Sigman and Boyle3, this hypothesis assumes that increased stratification in the Antarctic zone (Fig. 1) was associated with reduced upwelling of deep waters around Antarctica, thereby allowing CO2 outgassing to be suppressed by biological production while also allowing biological production to decline, which is consistent with Antarctic sediment records4. We point out here, however, that the response of ocean eddies to increased Antarctic stratification can be expected to increase, rather than reduce, the upwelling rate of deep waters around Antarctica. The stratification hypothesis may have difficulty in accommodating eddy feedbacks on upwelling within the constraints imposed by reconstructions of winds and Antarctic-zone productivity in glacial periods.
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  • 16
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    Strong hemispheric coupling of glacial climate through continental freshwater discharge and ocean circulation (2004)
    Nature Publishing Group
    In:  Nature, 430 . pp. 851-856.
    Details
    Publication Date: 2017-03-07
    Description: The climate of the last glacial period was extremely variable, characterized by abrupt warming events in the Northern Hemisphere, accompanied by slower temperature changes in Antarctica and variations of global sea level. It is generally accepted that this millennial-scale climate variability was caused by abrupt changes in the ocean thermohaline circulation. Here we use a coupled ocean–atmosphere–sea ice model to show that freshwater discharge into the North Atlantic Ocean, in addition to a reduction of the thermohaline circulation, has a direct effect on Southern Ocean temperature. The related anomalous oceanic southward heat transport arises from a zonal density gradient in the subtropical North Atlantic caused by a fast wave-adjustment process. We present an extended and quantitative bipolar seesaw concept that explains the timing and amplitude of Greenland and Antarctic temperature changes, the slow changes in Antarctic temperature and its similarity to sea level, as well as a possible time lag of sea level with respect to Antarctic temperature during Marine Isotope Stage 3.
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  • 17
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    Oceanic respite for wandering albatrosses (2000)
    Nature Publishing Group
    In:  Nature, 406 . pp. 955-956.
    Details
    Publication Date: 2021-07-01
    Description: Birds taking time off from breeding head for their favourite long-haul destinations. What oceanic seabirds do outside their breeding periods is something of a mystery, although altogether these "sabbaticals' add up to more than half of their lifetime and are probably a key feature of their life history. Here we use geolocation systems based on light-intensity measurements to show that during these periods wandering albatrosses (Diomedea exulans) leave the foraging grounds that they frequent while breeding for specific, individual oceanic sectors and spend the rest of the year there — each bird probably returns to the same area throughout its life. This discovery of individual home-range preferences outside the breeding season has important implications for the conservation of albatrosses threatened by the development of longline fisheries.
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  • 18
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    Iron and phosphorus co-limit nitrogen fixation in the eastern tropical North Atlantic (2004)
    Nature Publishing Group
    In:  Nature, 429 . pp. 292-294.
    Details
    Publication Date: 2017-03-10
    Description: The role of iron in enhancing phytoplankton productivity in high nutrient, low chlorophyll oceanic regions was demonstrated first through iron-addition bioassay experiments1 and subsequently confirmed by large-scale iron fertilization experiments2. Iron supply has been hypothesized to limit nitrogen fixation and hence oceanic primary productivity on geological timescales3, providing an alternative to phosphorus as the ultimate limiting nutrient4. Oceanographic observations have been interpreted both to confirm and refute this hypothesis5, 6, but direct experimental evidence is lacking7. We conducted experiments to test this hypothesis during the Meteor 55 cruise to the tropical North Atlantic. This region is rich in diazotrophs8 and strongly impacted by Saharan dust input9. Here we show that community primary productivity was nitrogen-limited, and that nitrogen fixation was co-limited by iron and phosphorus. Saharan dust addition stimulated nitrogen fixation, presumably by supplying both iron and phosphorus10, 11. Our results support the hypothesis that aeolian mineral dust deposition promotes nitrogen fixation in the eastern tropical North Atlantic.
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  • 19
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    Deep Roots of the Messinian Salinity Crisis (2003)
    Nature Publishing Group
    In:  Nature, 422 . pp. 602-606.
    Details
    Publication Date: 2019-09-23
    Description: The Messinian salinity crisis—the desiccation of the Mediterranean Sea between 5.96 and 5.33 million years (Myr) ago1—was one of the most dramatic events on Earth during the Cenozoic era2. It resulted from the closure of marine gateways between the Atlantic Ocean and the Mediterranean Sea, the causes of which remain enigmatic. Here we use the age and composition of volcanic rocks to reconstruct the geodynamic evolution of the westernmost Mediterranean from the Middle Miocene epoch to the Pleistocene epoch (about 12.1–0.65 Myr ago). Our data show that a marked shift in the geochemistry of mantle-derived volcanic rocks, reflecting a change from subduction-related to intraplate-type volcanism, occurred between 6.3 and 4.8 Myr ago, largely synchronous with the Messinian salinity crisis. Using a thermomechanical model, we show that westward roll back of subducted Tethys oceanic lithosphere and associated asthenospheric upwelling provides a plausible mechanism for producing the shift in magma chemistry and the necessary uplift (approx1 km) along the African and Iberian continental margins to close the Miocene marine gateways, thereby causing the Messinian salinity crisis.
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  • 20
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    Managing fisheries in a changing climate (2004)
    Nature Publishing Group
    In:  Nature, 429 .
    Details
    Publication Date: 2017-03-10
    Description: No need to wait for more information: industrialized fishing is already wiping out stocks.
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  • 21
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    Polysaccharide aggregation as a potential sink of marine dissolved organic carbon (2004)
    Nature Publishing Group
    In:  Nature, 428 . pp. 929-932.
    Details
    Publication Date: 2019-09-23
    Description: The formation and sinking of biogenic particles mediate vertical mass fluxes and drive elemental cycling in the ocean1. Whereas marine sciences have focused primarily on particle production by phytoplankton growth, particle formation by the assembly of organic macromolecules has almost been neglected2, 3. Here we show, by means of a combined experimental and modelling study, that the formation of polysaccharide particles is an important pathway to convert dissolved into particulate organic carbon during phytoplankton blooms, and can be described in terms of aggregation kinetics. Our findings suggest that aggregation processes in the ocean cascade from the molecular scale up to the size of fast-settling particles, and give new insights into the cycling and export of biogeochemical key elements such as carbon, iron and thorium.
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  • 22
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    Effect of trace metal availability on coccolithophorid calcification (2004)
    Nature Publishing Group
    In:  Nature, 430 . pp. 673-676.
    Details
    Publication Date: 2019-09-23
    Description: The deposition of atmospheric dust into the ocean has varied considerably over geological time1, 2. Because some of the trace metals contained in dust are essential plant nutrients which can limit phytoplankton growth in parts of the ocean, it has been suggested that variations in dust supply to the surface ocean might influence primary production3, 4. Whereas the role of trace metal availability in photosynthetic carbon fixation has received considerable attention, its effect on biogenic calcification is virtually unknown. The production of both particulate organic carbon and calcium carbonate (CaCO3) drives the ocean's biological carbon pump. The ratio of particulate organic carbon to CaCO3 export, the so-called rain ratio, is one of the factors determining CO2 sequestration in the deep ocean. Here we investigate the influence of the essential trace metals iron and zinc on the prominent CaCO3-producing microalga Emiliania huxleyi. We show that whereas at low iron concentrations growth and calcification are equally reduced, low zinc concentrations result in a de-coupling of the two processes. Despite the reduced growth rate of zinc-limited cells, CaCO3 production rates per cell remain unaffected, thus leading to highly calcified cells. These results suggest that changes in dust deposition can affect biogenic calcification in oceanic regions characterized by trace metal limitation, with possible consequences for CO2 partitioning between the atmosphere and the ocean.
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  • 23
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    Directly measured mid-depth circulation in the northeastern North Atlantic Ocean (2002)
    Nature Publishing Group
    In:  Nature, 419 . pp. 603-607.
    Details
    Publication Date: 2017-03-07
    Description: The circulation of water masses in the northeastern North Atlantic Ocean has a strong influence on global climate owing to the northward transport of warm subtropical water to high latitudes1. But the ocean circulation at depths below the reach of satellite observations is difficult to measure, and only recently have comprehensive, direct observations of whole ocean basins been possible2, 3, 4. Here we present quantitative maps of the absolute velocities at two levels in the northeastern North Atlantic as obtained from acoustically tracked floats. We find that most of the mean flow transported northward by the Gulf Stream system at the thermocline level (about 600 m depth) remains within the subpolar region, and only relatively little enters the Rockall trough or the Nordic seas. Contrary to previous work5, 6, our data indicate that warm, saline water from the Mediterranean Sea reaches the high latitudes through a combination of narrow slope currents and mixing processes. At both depths under investigation, currents cross the Mid-Atlantic Ridge preferentially over deep gaps in the ridge, demonstrating that sea-floor topography can constrain even upper-ocean circulation patterns.
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  • 24
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    Meandering of the subtropical front south-east of the Azores (1982)
    Nature Publishing Group
    In:  Nature, 300 (5889). pp. 245-246.
    Details
    Publication Date: 2018-03-08
    Description: A subtropical front was observed in the area south and southeast of the Azores during cruises of FS Meteor and FS Poseidon in early 1982. The front has a basically west–east extension, with considerable meandering observed. Meso-scale eddies are found on both sides. The overall flow pattern corresponds to earlier results on geopotential differences in the upper northeast Atlantic, but the baroclinic transport of the order of 107 m3 s−1 is found to be concentrated in a 60-km wide jet. We suggest here that the current band is part of the gyre circulation, resulting from a branching of the North Atlantic Current.
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  • 25
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    Fluxes of biogenic components from sediment trap deployment in circumpolar waters of the Drake Passage (1982)
    Nature Publishing Group
    In:  Nature, 299 (5879). pp. 145-147.
    Details
    Publication Date: 2019-01-21
    Description: Circumpolar surface waters dominate the circulation of the Southern Ocean and sustain one of the ocean's largest standing stocks of biomass thereby producing a significant output of biogenic components, mainly diatoms, to the bottom sediments. Generally transit of biogenic matter from the sea surface to the sea floor affects nutrient regeneration fuels benthic life and transfers signals to the sediment record1–5. Reliable quantification of the relationship between biological production, fractionation of skeletal and tissue components and bottom sediment accumulation depends on direct vertical flux measurements from sediment trap deployments6–9, which have proved to be most scientifically productive10–13. We now present data on vertical mass fluxes from the Southern Ocean and evidence for strong biogeochemical fractionation between organic carbon-, nitrogen- and phosphorus-containing compounds, siliceous and calcareous skeletal remains, and refractory aluminosilicates.
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    Glacial and interglacial wind regimes over the eastern subtropical Atlantic and North-West Africa (1981)
    Nature Publishing Group
    In:  Nature, 293 (5829). pp. 193-196.
    Details
    Publication Date: 2016-09-02
    Description: Analysis of aeolo-marine dust deposits in the subtropical eastern Atlantic enables the strength of the major wind patterns during the late Quaternary to be evaluated and gives an insight into the climate of North Africa.
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    Global change: Monsoon linkages (2003)
    Nature Publishing Group
    In:  Nature, 421 (6921). pp. 324-325.
    Details
    Publication Date: 2016-07-19
    Description: An excellent sediment record from the Arabian Sea traces recent patterns in the activity of the Asian monsoon. It reveals both variability in monsoon strength and links with climatic events elsewhere. The monsoon is the main determinant of environmental conditions over much of Asia, and so affects the most densely populated region on Earth. Differential heating of the north Indian Ocean and the northwest Pacific, and of the Asian land-mass, cause the seasonal reversal of monsoon winds. In summer, these winds blow northwards over the northern Indian Ocean, carrying huge amounts of moisture over the neighbouring land. The ensuing heavy rainfall can have devastating consequences for human life and livelihood. Conversely, agriculture in Asia depends on monsoon rains; and the seasonal upwelling of nutrient-laden subsurface waters, driven by monsoon winds, is essential to the success of coastal fisheries.
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  • 28
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    Magmatic and amagmatic seafloor generation at the ultraslow-spreading Gakkel ridge, Arctic Ocean (2003)
    Nature Publishing Group
    In:  Nature, 423 (6943). pp. 956-961.
    Details
    Publication Date: 2016-07-19
    Description: A high-resolution mapping and sampling study of the Gakkel ridge was accomplished during an international ice-breaker expedition to the high Arctic and North Pole in summer 2001. For this slowest-spreading endmember of the global mid-ocean-ridge system, predictions were that magmatism should progressively diminish as the spreading rate decreases along the ridge, and that hydrothermal activity should be rare. Instead, it was found that magmatic variations are irregular, and that hydrothermal activity is abundant. A 300-kilometre-long central amagmatic zone, where mantle peridotites are emplaced directly in the ridge axis, lies between abundant, continuous volcanism in the west, and large, widely spaced volcanic centres in the east. These observations demonstrate that the extent of mantle melting is not a simple function of spreading rate: mantle temperatures at depth or mantle chemistry (or both) must vary significantly along-axis. Highly punctuated volcanism in the absence of ridge offsets suggests that first-order ridge segmentation is controlled by mantle processes of melting and melt segregation. The strong focusing of magmatic activity coupled with faulting may account for the unexpectedly high levels of hydrothermal activity observed.
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    Power from the deep (2002)
    Nature Publishing Group
    In:  Nature Biotechnology, 20 (8). pp. 788-789.
    Details
    Publication Date: 2019-10-22
    Description: normous amounts of potential energy lie buried in marine sediments in the form of reduced carbon compounds. The most familiar form of this vast energy reserve is petroleum, which drives the lion's share of today's energy economy. The next most obvious submarine energy reserve, even more abundant than petroleum, is methane. At deep-sea conditions of low temperature and high pressure, large amounts of this natural gas are found in sub-seafloor reservoirs of frozen methane hydrates [1]. Yet there is another abundant, but less obvious, marine energy reserve: sediment-associated organic carbon, which represents about 2% of the dry weight of marine sediments along continental margins. Is it possible to tap into this vast, dispersed form of submarine energy? If so, how? The answer, in part, is that microbes already have tapped into this large energy reserve. Now, in two papers, one in this issue [2] and the other in a previous issue of Science [3], researchers harness microbially generated power by constructing a fuel cell that can exploit the naturally occurring voltage gradient created by microbial activity in marine sediments.
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  • 30
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    Mantle thermal pulses below the Mid-Atlantic Ridge and temporal variations in the formation of oceanic lithosphere (2003)
    Nature Publishing Group
    In:  Nature, 423 (6939). pp. 499-505.
    Details
    Publication Date: 2019-02-26
    Description: A 20-Myr record of creation of oceanic lithosphere is exposed along a segment of the central Mid-Atlantic Ridge on an uplifted sliver of lithosphere. The degree of melting of the mantle that is upwelling below the ridge, estimated from the chemistry of the exposed mantle rocks, as well as crustal thickness inferred from gravity measurements, show oscillations of ∼3–4 Myr superimposed on a longer-term steady increase with time. The time lag between oscillations of mantle melting and crustal thickness indicates that the mantle is upwelling at an average rate of ∼25 mm yr-1, but this appears to vary through time. Slow-spreading lithosphere seems to form through dynamic pulses of mantle upwelling and melting, leading not only to along-axis segmentation but also to across-axis structural variability. Also, the central Mid-Atlantic Ridge appears to have become steadily hotter over the past 20 Myr, possibly owing to north–south mantle flow.
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  • 31
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    Harnessing microbially generated power on the seafloor (2002)
    Nature Publishing Group
    In:  Nature Biotechnology, 20 (8). pp. 821-825.
    Details
    Publication Date: 2019-10-22
    Description: In many marine environments, a voltage gradient exists across the water sediment interface resulting from sedimentary microbial activity. Here we show that a fuel cell consisting of an anode embedded in marine sediment and a cathode in overlying seawater can use this voltage gradient to generate electrical power in situ. Fuel cells of this design generated sustained power in a boat basin carved into a salt marsh near Tuckerton, New Jersey, and in the Yaquina Bay Estuary near Newport, Oregon. Retrieval and analysis of the Tuckerton fuel cell indicates that power generation results from at least two anode reactions: oxidation of sediment sulfide (a by-product of microbial oxidation of sedimentary organic carbon) and oxidation of sedimentary organic carbon catalyzed by microorganisms colonizing the anode. These results demonstrate in real marine environments a new form of power generation that uses an immense, renewable energy reservoir (sedimentary organic carbon) and has near-immediate application.
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    Biogeography of the Indonesian coelacanths (2000)
    Nature Publishing Group
    In:  Nature, 403 (6765). p. 38.
    Details
    Publication Date: 2019-11-11
    Description: Living coelacanths (Latimeria chalumnae) are normally found only in the western Indian Ocean, where they inhabit submarine caves in the Comores Islands1. Two specimens have since been caught off the island of Manado Tua, north Sulawesi, Indonesia, some 10,000 kilometres away2. We sought to determine the ecological and geographic distribution of Indonesian coelacanth populations with a view to drawing up conservation measures for this extremely rare fish2,3. During our explorations, we discovered two living Indonesian coelacanths 360 km southwest of Manado Tua.
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  • 33
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    The first fossil cephalopod statoliths to be described from Europe (1980)
    Nature Publishing Group
    In:  Nature, 287 (5783). pp. 628-630.
    Details
    Publication Date: 2016-11-15
    Description: Statoliths of cephalopods are small, hard calcareous stones which lie within the cartilaginous skulls of octopods, sepioids and teuthoids1. Fossil statoliths, clearly belonging to genera which are alive today, have previously been described from 11 Cenozoic deposits spanning from the Eocene to the Pleistocene in North America2–5. Such statoliths are of particular interest because they provide a means of studying the evolution of living cephalopod groups which have no calcareous shells, including the cosmopolitan and numerous teuthoids and octopods. Here, the first cephalopod statoliths to be recognized in European deposits are described and identified as Loligo sp. They are compared with the North American fossil Loligo species and statoliths removed from the two living Loligo species of Europe.
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  • 34
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    Mantle plume noble gas component in glassy basalts from Reykjanes Ridge (1983)
    Nature Publishing Group
    In:  Nature, 305 (5933). pp. 403-407.
    Details
    Publication Date: 2016-11-23
    Description: Basalts from the Reykjanes Ridge contain noble gases delivered from the non-degassed lower mantle by the Iceland plume. These lower mantle gases are thought to be a mixture of planetary and solar components, as would be expected if the Earth accreted from fine silicate particles.
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    Turned out nice again (2000)
    Nature Publishing Group
    In:  Nature, 404 (6780). p. 814.
    Details
    Publication Date: 2021-02-25
    Description: Book review of: The Change in the Weather: People, Weather, and the Science of Climate by William K. Stevens Delacorte: 2000. 432 pp. $24.95
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    Earth science: The ultraslow difference (2003)
    Nature Publishing Group
    In:  Nature, 426 (6965). p. 401.
    Details
    Publication Date: 2017-03-07
    Description: The speed at which mid-ocean ridges grind out new ocean floor varies considerably. The slowest-spreading ridges are especially tough to study — but the latest data show that they are especially intriguing.
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  • 37
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    Bacterial growth and primary production along a north-south transect of the Atlantic Ocean (2002)
    Nature Publishing Group
    In:  Nature, 416 . pp. 168-171.
    Details
    Publication Date: 2017-02-28
    Description: The oceanic carbon cycle is mainly determined by the combined activities of bacteria and phytoplankton, but the interdependence of climate, the carbon cycle and the microbes is not well understood. To elucidate this interdependence, we performed high-frequency sampling of sea water along a north-south transect of the Atlantic Ocean. Here we report that the interaction of bacteria and phytoplankton is closely related to the meridional profile of water temperature, a variable directly dependent on climate. Water temperature was positively correlated with the ratio of bacterial production to primary production, and, more strongly, with the ratio of bacterial carbon demand to primary production. In warm latitudes (25 degrees N to 30 degrees S), we observed alternating patches of predominantly heterotrophic and autotrophic community metabolism. The calculated regression lines (for data north and south of the Equator) between temperature and the ratio of bacterial production to primary production give a maximum value for this ratio of 40% in the oligotrophic equatorial regions. Taking into account a bacterial growth efficiency of 30%, the resulting area of net heterotrophy (where the bacterial carbon demand for growth plus respiration exceeds phytoplankton carbon fixation) expands from 8 degrees N (27 degrees C) to 20 degrees S (23 degrees C). This suggests an output of CO2 from parts of the ocean to the atmosphere.
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    A mesoscale phytoplankton bloom in the polar Southern Ocean stimulated by iron fertilization (2000)
    Nature Publishing Group
    In:  Nature, 407 . pp. 695-702.
    Details
    Publication Date: 2017-02-28
    Description: Changes in iron supply to oceanic plankton are thought to have a significant effect on concentrations of atmospheric carbon dioxide by altering rates of carbon sequestration, a theory known as the 'iron hypothesis'. For this reason, it is important to understand the response of pelagic biota to increased iron supply. Here we report the results of a mesoscale iron fertilization experiment in the polar Southern Ocean, where the potential to sequester iron-elevated algal carbon is probably greatest. Increased iron supply led to elevated phytoplankton biomass and rates of photosynthesis in surface waters, causing a large drawdown of carbon dioxide and macronutrients, and elevated dimethyl sulphide levels after 13 days. This drawdown was mostly due to the proliferation of diatom stocks. But downward export of biogenic carbon was not increased. Moreover, satellite observations of this massive bloom 30 days later, suggest that a sufficient proportion of the added iron was retained in surface waters. Our findings demonstrate that iron supply controls phytoplankton growth and community composition during summer in these polar Southern Ocean waters, but the fate of algal carbon remains unknown and depends on the interplay between the processes controlling export, remineralisation and timescales of water mass subduction.
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    A marine microbial consortium apparently mediating abaerobic oxidation of methane (2000)
    Nature Publishing Group
    In:  Nature, 407 . pp. 623-626.
    Details
    Publication Date: 2017-02-28
    Description: A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments. Strong geochemical evidence for net methane consumption in anoxic sediments is based on methane profiles, radiotracer experiments and stable carbon isotope data. But the elusive microorganisms mediating this reaction have not yet been isolated, and the pathway of anaerobic oxidation of methane is insufficiently understood. Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria. Here we provide microscopic evidence for a structured consortium of archaea and sulphate-reducing bacteria, which we identified by fluorescence in situ hybridization using specific 16S rRNA-targeted oligonucleotide probes. In this example of a structured archaeal-bacterial symbiosis, the archaea grow in dense aggregates of about 100 cells and are surrounded by sulphate-reducing bacteria. These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane.
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    Rapid worldwide depletion of predatory fish communities (2003)
    Nature Publishing Group
    In:  Nature (423). pp. 280-283.
    Details
    Publication Date: 2017-03-07
    Description: Serious concerns have been raised about the ecological effects of industrialized fishing1, 2, 3, spurring a United Nations resolution on restoring fisheries and marine ecosystems to healthy levels4. However, a prerequisite for restoration is a general understanding of the composition and abundance of unexploited fish communities, relative to contemporary ones. We constructed trajectories of community biomass and composition of large predatory fishes in four continental shelf and nine oceanic systems, using all available data from the beginning of exploitation. Industrialized fisheries typically reduced community biomass by 80% within 15 years of exploitation. Compensatory increases in fast-growing species were observed, but often reversed within a decade. Using a meta-analytic approach, we estimate that large predatory fish biomass today is only about 10% of pre-industrial levels. We conclude that declines of large predators in coastal regions5 have extended throughout the global ocean, with potentially serious consequences for ecosystems5, 6, 7. Our analysis suggests that management based on recent data alone may be misleading, and provides minimum estimates for unexploited communities, which could serve as the 'missing baseline'8 needed for future restoration efforts.
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    Reduced calcification of marine plankton in response to increased atmospheric CO2 (2000)
    Nature Publishing Group
    In:  Nature, 407 . pp. 634-637.
    Details
    Publication Date: 2017-02-28
    Description: The formation of calcareous skeletons by marine planktonic organisms and their subsequent sinking to depth generates a continuous rain of calcium carbonate to the deep ocean and underlying sediments1. This is important in regulating marine carbon cycling and ocean–atmosphere CO2 exchange2. The present rise in atmospheric CO2 levels3 causes significant changes in surface ocean pH and carbonate chemistry4. Such changes have been shown to slow down calcification in corals and coralline macroalgae5,6, but the majority of marine calcification occurs in planktonic organisms. Here we report reduced calcite production at increased CO2 concentrations in monospecific cultures of two dominant marine calcifying phytoplankton species, the coccolithophorids Emiliania huxleyi and Gephyrocapsa oceanica . This was accompanied by an increased proportion of malformed coccoliths and incomplete coccospheres. Diminished calcification led to a reduction in the ratio of calcite precipitation to organic matter production. Similar results were obtained in incubations of natural plankton assemblages from the north Pacific ocean when exposed to experimentally elevated CO2 levels. We suggest that the progressive increase in atmospheric CO2 concentrations may therefore slow down the production of calcium carbonate in the surface ocean. As the process of calcification releases CO2 to the atmosphere, the response observed here could potentially act as a negative feedback on atmospheric CO2 levels.
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  • 42
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    Giant squids may die when exposed to warm water currents (1983)
    Nature Publishing Group
    In:  Nature, 303 (5916). pp. 422-423.
    Details
    Publication Date: 2019-04-16
    Description: Strandings of the giant squid, Architeuthis monachus (Steen-strup), have always stirred attention because of the rarity and enormous size of these cephalopods. These animals have never been observed in their natural habitat and little is known about their physiology and ecology. Stranding of giant squids in Newfoundland waters has been correlated with the inflow of warm water, suggesting that increased temperature may be causing their death1. Squids have also been carried to the Norwegian coast with the warm North Atlantic current2 and on 23 August 1982 a live specimen was caught off Radöy near Bergen, Norway (Fig. 1). This catch gave an unprecedented opportunity to study the effects of temperature on the oxygen binding properties of blood from the giant squid. The present finding of an excess of a fourfold decrease in O2 affinity when temperature is increased from 6.4 to 15°C strongly suggests that giant squids may suffocate from arterial desaturation when increased ambient temperatures are experierced.
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    Glaciology: Enigmatic Arctic ice sheets (2001)
    Nature Publishing Group
    In:  Nature, 410 (6827). pp. 427-428.
    Details
    Publication Date: 2017-02-28
    Description: To what extent was the Arctic Ocean glaciated in the past? Heavily, according to data, gathered by a submarine, which show considerable ice-scouring of topography in parts of the ocean basin
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    Bending-related faulting and mantle serpentinization at the Middle America Trench (2003)
    Nature Publishing Group
    Details
    Publication Date: 2023-09-26
    Description: The dehydration of subducting oceanic crust and upper mantle has been inferred both to promote the partial melting leading to arc magmatism and to induce intraslab intermediate-depth earthquakes, at depths of 50–300 km. Yet there is still no consensus about how slab hydration occurs or where and how much chemically bound water is stored within the crust and mantle of the incoming plate. Here we document that bending-related faulting of the incoming plate at the Middle America trench creates a pervasive tectonic fabric that cuts across the crust, penetrating deep into the mantle. Faulting is active across the entire ocean trench slope, promoting hydration of the cold crust and upper mantle surrounding these deep active faults. The along-strike length and depth of penetration of these faults are also similar to the dimensions of the rupture area of intermediate-depth earthquakes.
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  • 45
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray diffraction analysis of the Saccharomyces cerevisiae Ran-binding protein Mog1p (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 229-231 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mog1p binds the Ras-family GTPase Ran/Gsp1p, which has a central role in nucleocytoplasmic transport and cell-cycle progression. Overexpression of MOG1 is able to suppress temperature-sensitive gsp1 mutants in yeast; Δmog1 null mutants display temperature-sensitive defects in nuclear trafficking. Orthorhombic crystals of bacterially expressed Mog1p that diffract to beyond 2 Å resolution using synchrotron radiation have been obtained. The crystals have P212121 symmetry, with unit-cell parameters a = 39.67, b = 51.96, c = 112.23 Å, a Matthews coefficient of 2.44 Å3 Da−1, an estimated solvent content of 49.5% and one chain in the asymmetric unit.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999016856
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  • 46
    Electronic Resource
    Electronic Resource
    Crystal structure of δ-chymotrypsin bound to a peptidyl chloromethyl ketone inhibitor (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 280-286 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Chymotrypsin is a member of the trypsin family of serine proteases and is one of the first proteins successfully studied by X-ray crystallography. It is secreted into the intestine as the inactive precursor chymotrypsinogen; four sequential cleavages of the peptide bonds following residues 13, 15, 146 and 148 occur to generate the active π, δ, κ and α forms of chymotrypsin. 13C NMR has shown [O'Connell & Malthouse (1995). Biochem. J. 307, 353–359] that when the δ form of chymotrypsin is inhibited by 2-13C-enriched benzyloxycarbonylglycylglycylphenylalanyl chloromethane, a tetrahedral adduct is formed which is thought to be analogous to the tetrahedral intermediate formed during catalysis. This inhibitor complex has been crystallized as a dimer in space group P41212. The structure has been refined at 2.14 Å resolution to an R value of 21.2% (free R = 25.2%). Conformational differences between δ-chymotrypsin and chymotrypsinogen in the region of the flexible autolysis loop (residues 145–150) were observed. This is the first crystal structure of δ-chymotrypsin and includes two residues which are disordered in previous crystal structures of active chymotrypsin. A difference of 11.3 Å2 between the average B values of the monomers within the asymmetric unit is caused by lattice-disordering effects approximating to rotation of the molecules about a crystallographic screw axis. The substrate-binding mode of the inhibitor was similar to other chymotrypsin peptidyl inhibitor complexes, but this is the first published chymotrypsin structure in which the tetrahedral chloromethyl ketone transition-state analogue is observed. This structure is compared with that of a similar tetrahedral transition-state analogue which does not alkylate the active-site histidine residue.
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    URL: http://dx.doi.org/10.1107/S0907444999016583
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  • 47
    Electronic Resource
    Electronic Resource
    Properties of an electron-density map derived from a limited number of experimentally determined triplet phases (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 322-327 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In a previous communication [Weckert et al. (1999). Acta Cryst. D55, 1320–1328], the feasibility of the measurement of a large set of triplet phases by three-beam interference was demonstrated. This paper reports the methodology for the calculation of an electron-density map from this limited amount of experimental phase information and the map's properties with respect to model building and refinement. The tetragonal form of hen egg-white lysozyme (HEWL) was chosen as a test structure for the development of this method. The quality of the electron-density map obtained from all measured triplet phases allows a straightforward and nearly complete interpretation. The starting model was refined to a final R value of 17.4%. In a second step, the minimum number of phased reflections needed for the interpretation of an electron-density map was investigated, applying criteria based on |F| and resolution.
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    URL: http://dx.doi.org/10.1107/S0907444999016716
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  • 48
    Electronic Resource
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    Crystallization and preliminary X-ray study of β-mannosidase from Trichoderma reesei (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 342-343 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: β-Mannosidase from Trichoderma reesei, a 105 kDa glycoprotein, has been crystallized. The crystals belong to the space group P41212 or P43212, with unit-cell dimensions a = b = 165.86, c = 122.46 Å, and diffract beyond 2.75 Å resolution. X-ray diffraction data were collected from a frozen crystal on a synchrotron X-ray source.
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    URL: http://dx.doi.org/10.1107/S0907444999016625
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  • 49
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    Purification, crystallization and X-ray analysis of crystals of pectate lyase A from Erwinia chrysanthemi (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 351-353 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pectate lyase A is secreted by Erwinia chrysanthemi and is a virulence factor for soft rot diseases in plants. Crystals of pectate lyase A were obtained by vapor-diffusion techniques in the presence of polyethylene glycol. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 48.96, b = 148.86, c = 78.61 Å, β = 97.32°. The crystals contain two protein molecules of 38 kDa per asymmetric unit and diffract to 2.4 Å using Cu Kα radiation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999016807
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  • 50
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    Crystallization and preliminary X-ray analysis of the catalytic domain of the adenylate cyclase GRESAG4.1 from Trypanosoma brucei (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 359-362 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Adenylate cyclases (ACs) are involved in signal transduction by generating the second messenger, cAMP. In Trypanosoma brucei, 3′,5′-cyclic adenosine monophosphate (cAMP) controls the life cycle of this unicellular parasite. cAMP is generated by a class of adenylate cyclases which are either constitutively (GRESAG4.1–4.3) or transiently expressed (ESAG4) during the life cycle. Unlike mammalian ACs, the trypanosomal ACs have a simple topology comprising of a large extracellular region, a transmembrane helix and a cytosolic catalytic region. Two orthorhombic crystal forms of the catalytic AC domain of GRESAG4.1 (residues Ala884–Thr1132) were generated by the hanging-drop vapour-diffusion method. X-ray diffraction data from GRESAG4.1 crystals were collected at 1.9 Å resolution using synchrotron radiation. Furthermore, two heavy-metal derivative data sets were collected from crystal form A; heavy-atom sites were subsequently located in difference Patterson maps.
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    Crystallization and preliminary X-ray diffraction analysis of β-cinnamomin, an elicitin secreted by the phytopathogenic fungus Phytophthora cinnamomin (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 363-365 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cinnamomin (CIN) belongs to a family of 10 kDa proteins designated as elicitins. Some of these proteins induce a hypersensitive response in diverse plant species, leading to resistance against fungal and bacterial plant pathogens. CIN was crystallized by the vapour-diffusion method using either ammonium sulfate or polyethyleneglycol (PEG) as precipitants in solutions buffered at around pH 7. These crystals are isomorphous and belong to the triclinic space group, with unit-cell parameters a = 31.69, b = 36.99, c = 44.09 Å, α = 76.86, β = 84.41, γ = 80.26°. A frozen crystal diffracted X-rays beyond 1.45 Å resolution on a synchrotron-radiation source.
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    Crystallization and preliminary X-ray diffraction analysis of the NAD-dependent non-phosphorylating GAPDH of the hyperthermophilic archaeon Thermoproteus tenax (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 89-91 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant non-phosphorylating NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN) of the hyperthermophilic crenarchaeote Thermoproteus tenax has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion technique. Crystals of different habits were obtained from several precipitant solutions (salts and polyethylene glycols). Preliminary X-ray analysis was performed with crystals grown in ammonium formate, which belonged to the primitive hexagonal space group P622, and had unit-cell parameters a = b = 184.8, c = 133.0 Å, γ = 120°. Assuming a molecular weight of 55 kDa, a Matthews parameter of 3.3 Å3 Da−1 is calculated assuming two molecules per asymmetric unit. The diffraction limit of these crystals is 2.5 Å resolution.
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    Structure of the Ser195Ala mutant of human α-thrombin complexed with fibrinopeptide A(7–16): evidence for residual catalytic activity (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 406-410 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Ser195Ala mutant of human α-thrombin was complexed with fibrinopeptide A(7–22) (FPA) in an effort to describe the (P1′–P6′) post-cleavage binding subsites of the fibrinogen-recognition exosite and define more clearly the nature of the Michaelis complex and the scissile peptide bond bound at the catalytic site. The thrombin mutant, however, has residual catalytic activity and proteolysis occurred at the Arg16–Gly17 bond. Thus, the structure of the thrombin complex determined was that of FPA(7–16) bound at the active site, which is very similar to the ternary FPA(7–16)cmk–human thrombin–hirugen complex (r.m.s.d. ∼ 0.4 Å; Stubbs et al., 1992). It is further shown by subsidiary experiments that the cleavage is the result of residual catalytic activity of the altered catalytic machinery.
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    Crystallization of the NADP-dependent β-keto acyl-carrier protein reductase from Brassica napus (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 86-88 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The NADP-dependent β-keto acyl-carrier protein reductase (BKR) from Brassica napus has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol of average molecular weight 1500 as the precipitant. The crystals belong to the hexagonal space group P6422, with unit-cell parameters a = b = 129.9, c = 93.1 Å, α = β = 90, γ = 120°. Calculated values for Vm, the use of rotation and translation functions and consideration of the packing suggest that the asymmetric unit contains a monomer. The crystals diffract to beyond 2.8 Å resolution and are more amenable to X-ray diffraction analysis than those reported previously for the Escherichia coli enzyme. The structure determination of B. napus BKR will provide important insights into the catalytic mechanism of the enzyme and into the evolution of the fatty-acid elongation cycle by comparisons with the other oxidoreductase of the pathway, enoyl acyl-carrier protein reductase (ENR).
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    Purification, crystallization and preliminary X-ray analysis of haemoglobin I from the armoured catfish Liposarcus anisitsi (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 495-497 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Liposarcus anisitsi is an armoured catfish that presents accessorial air oxygenation through a modified stomach, which allows this species to survive in waters with very low oxygen content. Analysis of its haemolysate has shown the presence of four haemoglobins; this work focuses on the main component, haemoglobin I. It has been crystallized in two different forms and X-ray diffraction data have been collected to 2.77 and 2.86 Å resolution using synchrotron radiation. Crystals were determined to belong to the space groups C2 and P21 and preliminary structural analysis revealed the presence of one tetramer in the asymmetric unit in both crystal forms. The structure was determined using a standard molecular-replacement technique.
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    Crystallization and preliminary crystallographic studies of a new crystal form of Escherichia coliL-asparaginase II (Ser58Ala mutant) (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 509-511 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Periplasmic Escherichia coli L-asparaginase II with an Ser58Ala mutation in the active-site cavity has been crystallized in a new orthorhombic form (space group P21212). Crystals of this polymorph suitable for X-ray diffraction have been obtained by vapour diffusion using two sets of conditions: (i) 1% agarose gel using MPD as precipitant (pH 4.8) and (ii) liquid droplets using PEG-MME 550 (pH 9.0). The crystals grown in agarose gel are characterized by unit-cell parameters a = 226.9, b = 128.4, c = 61.9 Å and diffract to 2.3 Å resolution. The asymmetric unit contains six protein molecules arranged into one pseudo-222-symmetric homotetramer and an active-site competent dimer from which another homotetramer is generated by crystallographic symmetry.
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    Crystallization and preliminary X-ray analysis of shikimate dehydrogenase from Escherichia coli (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 512-515 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Shikimate dehydrogenase from Escherichia coli has been crystallized by the vapour-diffusion method using ammonium sulfate as a precipitant. Mass spectrometry confirmed the purity of the enzyme and dynamic light scattering was used to find the appropriate additives to yield a monodisperse enzyme solution. The crystals are monoclinic, space group C2, with unit-cell parameters a = 110.0, b = 139.8, c = 102.6 Å, β = 122.2° (at 100 K). Native crystals diffract to 2.3 Å in-house on a rotating-anode X-ray source. The asymmetric unit is likely to contain four molecules, related by 222 symmetry, corresponding to a packing density of 2.86 Å3 Da−1.
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    Crystallization and preliminary X-ray diffraction studies of a monooxygenase from Streptomyces coelicolor A3(2) involved in the biosynthesis of the polyketide actinorhodin (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 481-483 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The aromatic monooxygenase ActVA-Orf6 from Streptomyces coelicolor A3(2) that catalyses an unusual oxidation on the actinorhodin biosynthetic pathway has been crystallized. The crystals diffract to 1.73 Å and belong to space group P212121, with unit-cell parameters a = 46.95, b = 59.29, c = 71.67 Å. Solvent-content (44%) and self-rotation function calculations predict the presence of two molecules in the asymmetric unit. Structure determination should provide further insight into the enzyme mechanism and aid in the design of biosynthetic pathways to produce new polyketide natural products with novel functionality.
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    Crystallization of engineered Thermus flavus 5S rRNA under earth and microgravity conditions (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 498-500 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Thermus flavus 5S rRNA with a molecular weight of about 40 kDa was modified at the 5′ and 3′ ends. Crystals were obtained under earth and microgravity conditions. The best crystals were obtained during NASA space mission STS 94. For the first time, it was possible to collect a complete data set from 5S rRNA crystals to 7.8 Å resolution and to assign the space group as R32, with unit-cell parameters a = b = 110.3, c = 387.6 Å, α = β = 90, γ = 120°.
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    Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 506-508 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The small 62-residue IgG-binding domain B1 of protein L from Peptostreptococcus magnus (Ppl-B1) has proven to be a simple system for the study of the thermodynamics and kinetics of protein folding. X-ray diffraction studies have been initiated in order to determine how the thermostability, folding and unfolding rates of a series of point mutations spanning Ppl-B1 correlate with the high-resolution structures. To this end, a tryptophan-containing variant of Ppl-B1 (herein known as wild type) and two mutants, Lys61Ala and Val49Ala, have been crystallized. Full data sets have been collected for the wild type and the Lys61Ala and Val49Ala mutants to resolutions of 1.7, 2.3 and 1.8 Å, respectively. Interestingly, all three crystallize using different precipitants and in different space groups. This may be a consequence of the relatively large effects of single-site mutations on surface-charge distribution or structural conformation, which might affect crystal contact sites.
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    The porphobilinogen synthase family of metalloenzymes (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 115-128 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The porphobilinogen synthase (PBGS) family of enzymes catalyzes the first common step in the biosynthesis of the essential tetrapyrroles such as chlorophyll and porphyrin. Although PBGSs are highly conserved at all four levels of protein structure, there is considerable diversity in the use of divalent cations for the catalytically essential and allosteric roles. Assumptions regarding commonalities among the PBGS proteins coupled with the diversity of usage of metal ions has led to a confused literature. The recent publication of crystal structures for three PBGS proteins coupled with more than 50 individual PBGS sequences allows an evaluation of these assumptions. This topical review focuses on the usage of metals by the PBGS family of proteins. It raises doubt concerning a dogma that there has been an evolutionary shift between ZnII and MgII at one or more of the divalent metal-binding sites. It also raises the possibility that there may be up to four specific divalent metal ion-binding sites, each serving a unique function that can be alternatively filled by amino acids in some of the PBGSs.
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    β-Sheet propensity and its correlation withparameters based on conformation (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 589-594 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The dispersion of the main-chain and side-chain conformations in the φ, ψ, χ1 space for all residues have been estimated in terms of three parameters corresponding to the entropy (S) of the distribution, the volume (DV) and the area (DA) the points are enclosed in. These parameters are inversely correlated with Chou and Fasman β-sheet propensities, Pβ (Gly and Pro excluded), suggesting that residues with greater dispersion in the conformational space are weak β-sheet formers. It was also found that different residues have different relative populations in the bridging region (intervening between the helical and β-sheet regions) which may lie on the pathway for interconversion between α and β conformations. The energy barrier for this transformation, as obtained from the population of residues in the bridging region relative to the β region, is directly correlated to Pβ. Residues with high Pβ have branched side chains, which have greater steric interactions with the main-chain atoms resulting in a shrinking of the available conformational space (first correlation) and a steeper energy gradient beyond the allowed space (second correlation) compared with linear residues. It is proposed that if residues exist in an extended conformation when the polypeptide chain is synthesized, a stretch of residues with high Pβ, because of the high energy barrier for their conversion into the α conformation, will continue to remain in the extended conformation and will ultimately constitute a β-strand in the folded structure.
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    Wavelet analysis of electron-density maps (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 618-624 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The wavelet transform is a powerful technique in signal processing and image analysis and it is shown here that wavelet analysis of low-resolution electron-density maps has the potential to increase their resolution. Like Fourier analysis, wavelet analysis expresses the image (electron density) in terms of a set of orthogonal functions. In the case of the Fourier transform, these functions are sines and cosines and each one contributes to the whole of the image. In contrast, the wavelet functions (simply called wavelets) can be quite localized and may only contribute to a small part of the image. This gives control over the amount of detail added to the map as the resolution increases. The mathematical details are outlined and an algorithm which achieves a resolution increase from 10 to 7 Å using a knowledge of the wavelet-coefficient histograms, electron-density histogram and the observed structure amplitudes is described. These histograms are calculated from the electron density of known structures, but it seems likely that the histograms can be predicted, just as electron-density histograms are at high resolution. The results show that the wavelet coefficients contain the information necessary to increase the resolution of electron-density maps.
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    Crystallization and preliminary crystallographic analysis of Rieske iron–sulfur protein II (soxF) from Sulfolobus acidocaldarius (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 643-644 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An archaeal Rieske iron–sulfur protein has been crystallized for the first time. The genetically constructed soluble form of the soxF protein was expressed in E. coli. It contains a correctly inserted [2Fe–2S] cluster. The authentic soxF protein is part of a terminal oxidase complex in the respiratory chain of the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius (DSM 639). The enzyme crystallizes in the space group P61 or P65, with unit-cell parameters a = b = 80.19, c = 75.69 Å. A complete data set has been collected to 1.64 Å resolution at 100 K.
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    L-Isoaspartate 115 of porcine β-trypsin promotes crystallization of its complex with bdellastasin (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 581-588 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Bdellastasin is a 59-amino-acid, cysteine-rich, antistasin-type inhibitor of sperm acrosin, plasmin and trypsin, isolated from the medicinal leech Hirudo medicinalis. The complex formed between bdellastasin and porcine β-trypsin has previously been crystallized in the presence of PEG in a tetragonal crystal form of space group P43212 and has now been found to crystallize under high-salt conditions in the enantiomorphic space group P41212. These structures have been solved and refined to 2.8 and 2.7 Å resolution, respectively. Bdellastasin turns out to have an antistasin-like fold exhibiting a bis-domainal structure. In the second new crystal form, the flexible N-terminal subdomain is rotated with respect to the C-terminal subdomain by about 90°, fitting into a cavity formed by symmetry-related trypsin molecules. The canonical inhibitor–proteinase interaction is restricted to the primary binding loop comprising residues Leu31–Lys36 of bdellastasin. During the refinement, a bound sodium ion occupying the calcium-binding site of the porcine β-trypsin component was discovered. This sodium ion is coordinated in a tetragonal–pyramidal manner, with the geometry of the enclosing loop slightly changed compared with the loop in the presence of calcium. In the crystal form of space group P43212, the electron density for residue 115 of porcine β-trypsin clearly indicates the presence of a β-isomerized L-aspartic acid, which is placed in spatial proximity to segment Thr144–Gly148 of a symmetry-related trypsin molecule. This is the first structurally observed example of an L-isoaspartate in β-trypsin originating from Asn. A comparison with other known crystal structures of porcine β-trypsin–macromolecular inhibitor complexes suggests that the deamidation, isomerization and racemization of Asn115 is the key step in crystallization.
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    Crystallization and preliminary X-ray diffraction data of mouse L-chain apoferritin crystals (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 634-636 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of recombinant mouse L-chain apoferritin were obtained by the hanging-drop technique using ammonium sulfate as precipitant. Two crystal forms were observed in the same drop. The crystals belong to either the P2 monoclinic or to the P4212 tetragonal space group. The monoclinic crystals diffracted to beyond 2.4 Å resolution but were systematically twinned, while the tetragonal crystals diffracted to beyond 2.9 Å. These crystallization conditions in the absence of metal salts should facilitate the study of the interaction between L-chain ferritins and heavy metals, particularly the iron core.
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    Crystallization and preliminary X-ray study of Pk-REC from a hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1 (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 648-649 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pk-REC is a protein which binds to DNA and catalyzes the central step of recombination and repair. The protein was crystallized using the hanging-drop vapour-diffusion method with PEG as a precipitant. Two orthorhombic crystal forms I and II with the same space group P212121 were obtained at pH 8.0 using PEG 3000 and PEG 550 monomethylether, respectively. The unit-cell parameters were a = 151, b = 174, c = 241 Å for form I and a = 151, b = 176, c = 300 Å for form II, indicating that the asymmetric unit contains more than 20 molecules.
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    Crystallization and preliminary crystallographic study of cucurmosin, a ribosome-inactivating protein from the sarcocarp of Cucurbita moschata (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 665-666 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cucurmosin, a ribosome-inactivating protein purified from pumpkin, the sarcocarp of Cucurbita moschata, has been crystallized using polyethylene glycol as a precipitant. The crystals belong to space group P212121 and have unit-cell parameters a = 41.91, b = 59.48, c = 98.78 Å. There is one molecule in the asymmetric unit. The diffraction data to 3.0 Å resolution were collected on a MAR Research image-plate detector.
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    Crystallization and preliminary X-ray analysis of high-alkaline pectate lyase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 749-750 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pel-15, a high-alkaline pectate lyase (pectate transeliminase; E.C. 4.2.2.2) from Bacillus sp. strain KSM-P15, has been crystallized using the hanging-drop vapour-diffusion method at 277 K. Two different crystal forms were obtained and preliminary X-ray diffraction data were collected from each crystal form at 100 K. Both forms belong to the orthorhombic space group P212121 and contain one molecule per asymmetric unit. The unit-cell parameters of form I are a = 43.2 (2), b = 60.2 (2), c = 82.2 (2) Å and those of form II are a = 42.9 (1), b = 43.4 (1), c = 105.9 (3) Å. Diffraction data to a resolution of 1.5 Å were collected from form II crystals using a synchrotron-radiation source.
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    Ab initio structure determination of the lantibiotic mersacidin (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 705-713 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of mersacidin, a potential novel antibiotic against methicillin- and vancomycin-resistant Staphylococcus aureus strains, has been determined by ab initio methods. Despite all crystals being merohedrally twinned, an accurate structural model with an R value of 13.4% has been obtained at atomic resolution. With six molecules in the asymmetric unit and no atom heavier than sulfur, the structure corresponds to a protein of 120 amino acids and is the largest approximately equal-atom unknown structure solved by direct methods. In the crystal, the molecule assumes a compact fold different from that found by NMR in solution. Comparison of the NCS-related molecules reveals regions of variable flexibility. The region highly homologous to the related antibiotic actagardine is very rigid and possibly defines an essential building block of this class of new antibacterial substances.
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    Crystallization and preliminary crystallographic studies of a SAM domain at the C-terminus of human p73α (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 769-771 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: p73 is a recently discovered homologue of the tumour suppressor p53 and contains all three functional domains of p53. The α-splice variant of p73 (p73α) contains an additional structural domain near its C-terminus that has sequence homology with the sterile α-motif (SAM) domain. This domain is considered to be responsible for mediating protein–protein interactions. Pyramidal crystals of human p73α SAM domain were obtained by the hanging-drop vapour-diffusion method with ammonium dihydrogen orthophosphate as the precipitant. The crystals diffract to 2.54 Å resolution and belong to the tetragonal space group P41212, with unit-cell parameters a = b = 32.02, c = 133.84 Å. The structure was solved by molecular replacement using the NMR structure of the same protein as the search model.
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    Crystallization and preliminary X-ray crystallographic analysis of the 30 kDa membrane-binding domain of protein 4.1 from human erythrocytes (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 187-188 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The 30 kDa membrane-binding domain of protein 4.1 from human erythrocytes has been expressed in Escherichia coli and crystallized in a form suitable for X-ray crystallographic study. Crystals were grown using a salting-in technique. Crystals have a tetragonal plate shape and belong to the C2 space group, with unit-cell parameters a = 163.9, b = 106.5, c = 93.5 Å, β = 95.5°. The crystals diffract to 2.8 Å resolution.
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    Crystallization and preliminary X-ray analysis of human grancalcin, a novel cytosolic Ca2+-binding protein present in leukocytes (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 772-774 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant human grancalcin, a calcium-binding protein from leukocytes, has been crystallized in the presence or absence of Ca2+ by the vapor-diffusion method. Two crystal forms of apo grancalcin were obtained: space group P21, with unit-cell parameters a = 48.4, b = 81.1, c = 46.6 Å, β = 111.3°, diffracting to 1.9 Å, and space group C2, with unit-cell parameters a = 97.0, b = 51.9, c = 75.9 Å, β = 108.5°, diffracting to 2.4 Å. Crystals were also grown in the presence of 5 mM Ca2+. They also belong to space group C2, with unit-cell parameters a = 97.4, b = 50.3, c = 77.6 Å, β = 108.2°, which are very similar to the second apo grancalcin form. These crystals diffract to 2.5 Å.
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    Crystallization and preliminary X-ray diffraction analysis of Saccharomyces cerevisiae Ygr203p, a homologue of Acr2 arsenate reductase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 778-780 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Ygr203p, a 148-residue protein encoded by the ygr203w gene of Saccharomyces cerevisiae, is a homologue of the yeast Acr2 arsenate reductase encoded by the acr2 (or ypr200c) gene. It also shows significant sequence similarity to the human cell-cycle control Cdc25 phosphatase family. It has been overexpressed in soluble form in Escherichia coli with a His6 tag at its C-terminus. The recombinant protein has been crystallized at 296 K using sodium chloride as precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 40.48, b = 50.95, c = 91.95 Å. The asymmetric unit contains a monomer, giving a crystal volume per protein mass (Vm) of 2.61 Å3 Da−1 and a solvent content of 53.8%. The crystals diffract to better than 1.9 Å resolution with Cu Kα X-rays. They are therefore suitable for high-resolution structure determination.
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    Structure of m-carboxyphenyl-α-D-galactopyranoside complexed to heat-labile enterotoxin at 1.3 Å resolution: surprising variations in ligand-binding modes (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 795-804 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the quest to develop drugs against traveller's diarrhoea and cholera, the structure of the B pentamer of heat-labile enterotoxin (LT) complexed with a new receptor-binding antagonist, m-carboxyphenyl-α-D-galactopyranoside, has been determined. The high resolution obtained for this structure allowed anisotropic refinement of the model. It was also now possible to confirm at a near-atomic resolution the structural similarity between the B subunits of LT and the closely related cholera toxin (CT), including the similarity in deviations of planarity of the same peptide unit in LT and CT. The structure of the LT complex clearly revealed different conformations for the m-carboxyphenyl moiety of the ligand in the five B subunits of LT, while the binding modes of the well defined galactopyranoside moieties were identical. In two binding sites the m-carboxyphenyl moiety displayed no significant electron density, demonstrating significant flexibility of this moiety. In a third binding site the m-carboxyphenyl moiety could be modelled unambiguously into the density. The two remaining binding sites were involved in crystal packing contacts and the density for the ligands in these two binding sites clearly revealed different binding modes, of which one conformation was identical to and one completely different from the conformation of m-carboxyphenyl-galactopyranoside in the third subunit. The multiple binding modes observed in the crystal may represent the ensemble of conformations of m-carboxyphenyl-α-D-galactopyranoside complexed to LT in solution.
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    Eigensystem analysis of the refinement of a small metalloprotein (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 842-856 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The eigenvalues and eigenvectors of the least-squares normal matrix for the full-matrix refinement problem contain a great deal of information about the quality of a model; in particular the precision of the model parameters and correlations between those parameters. They also allow the isolation of those parameters or combinations of parameters which are not determined by the available data. Since a protein refinement is usually under-determined without the application of geometric restraints, such indicators of the reliability of a model offer an important contribution to structural knowledge. Eigensystem analysis is applied to the normal matrices for the refinement of a small metalloprotein using two data sets and models determined at different resolutions. The eigenvalue spectra reveal considerable information about the conditioning of the problem as the resolution varies. In the case of a restrained refinement, it also provides information about the impact of various restraints on the refinement. Initial results support conclusions drawn from the free R factor. Examination of the eigenvectors provides information about which regions of the model are poorly determined. In the case of a restrained refinement, it is also possible to isolate places where X-ray and geometric restraints are in disagreement, usually indicating a problem in the model.
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    Crystallization and preliminary X-ray studies of recombinant amylosucrase from Neisseria polysaccharea (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 203-205 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant amylosucrase from Neisseria polysaccharea was crystallized by the vapour-diffusion procedure in the presence of polyethylene glycol 6000. The crystals belong to the orthorhombic space group P21212, with unit-cell parameters a = 95.7, b = 117.2, c = 62.1 Å, and diffract to 1.6 Å resolution. A p-chloromercuribenzene sulfonate (pcmbs) derivative has been identified and a selenomethionine-substituted protein has been produced and crystallized.
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    Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 206-209 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Phosphonoacetaldehyde hydrolase, a C—P bond-cleaving enzyme which utilizes an unusual bicovalent catalytic strategy, has been crystallized by the hanging-drop vapor-diffusion method using PEG 4000 as the precipitant. The crystals belong to the monoclinic system and belong to space group C2, with unit-cell parameters a = 210.5, b = 45.5, c = 64.7 Å, β = 105.0°. The asymmetric unit contains a dimer related by a non-crystallographic dyad. In addition to a 2.7 Å native data set, the following data sets have been collected: a 2.4 Å data set from crystals complexed with the intermediate analog vinyl sulfonate, a 3.0 Å three-wavelength MAD data set from crystals complexed with the product analog WO_{4}^{2-}, as well as several heavy-atom data sets to 3.0 Å or better, of which only three have proven useful for MIR calculations. Examination of the native Patterson map revealed NCS that made previously uninterpretable derivative data useful. Independent phase sets were first calculated and refined for the MAD and MIR experiments separately and were then combined. The combined phase set was further improved by solvent flattening, histogram matching and NCS averaging. Interpretation of the resulting electron-density map is currently under way.
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    Crystallization and preliminary X-ray diffraction studies of a β-carbonic anhydrase from the red alga Porphyridium purpureum (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 210-211 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The β-carbonic anhydrase from the red alga Porphyridium purpureum was heterologously expressed, purified and crystallized. The crystals belong to space group P21 (unit-cell parameters a = 63.8, b = 113.9, c = 73.8 Å, β = 104.1°) with two subunits per asymmetric unit and diffract to 2.5 Å resolution.
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    Expression, crystallization and preliminary X-ray studies of the PDZ domain of Dishevelled protein (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 212-214 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Dishevelled (Dsh) protein is an important component of the Wnt signal-transduction pathway. It has three relatively conserved domains: DIX, PDZ and DEP. The PDZ domain of the Xenopus laevis homolog of Dsh, which consists of residues 254–348, was overexpressed as a soluble protein in Escherichia coli, purified and crystallized. The crystals were obtained by the vapor-diffusion method, using 1.4 M sodium formate as a precipitant. The crystals diffracted to 2.3 Å resolution. The space group was determined to be P6122 or P6522, with unit-cell dimensions a = b = 95.9, c = 93.9 Å.
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    Towards automated Laue data processing: application to the choice of optimal X-ray spectrum (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 973-985 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Laue data reduction has now reached a level of sophistication that allows nearly automated processing to be performed. The software described enables complete reduction of the data with essentially no user intervention, making Laue processing almost as straightforward as monochromatic data processing. Interactive work is limited to the indexing of only one Laue pattern. More importantly, it is shown that the data quality is substantially enhanced when soft-limited predictions are used. Further improvement obtained by taking advantage of the structure-factor amplitudes from a known closely related structure is described. To determine the most suitable type of insertion device to be used for time-resolved Laue crystallography, the technique described was applied to Laue data sets collected from photoactive yellow protein under identical conditions but with three different insertion devices: a wiggler, a broad-bandpass undulator and a single-line undulator. Although the optimal choice may ultimately be dictated by sample parameters (such as mosaic spread) and by the type of experiment (repeatable or non-repeatable reactions), the results here show that the use of single-line undulators will generally yield by far the best compromise between data quality, acquisition time and radiation damage.
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    Crystallization and diffraction to ultrahigh resolution (0.8 Å) of a designed variant of the Rop protein (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1015-1016 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Rop protein is the paradigm of a highly regular four-α-helix bundle and as such has been subject to numerous structural and mutagenesis studies. Crystals of a designed Rop variant which establishes a continuous heptad pattern through the bend region have been obtained by a combination of vapour-diffusion and seeding techniques. The crystals diffract to ultrahigh (0.8 Å) resolution using synchrotron radiation and cryogenic conditions.
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    The high-mosaicity illusion: revealing the true physical characteristics of macromolecular crystals (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 986-995 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Typical measurements of macromolecular crystal mosaicity are dominated by the characteristics of the X-ray beam and as a result the mosaicity value given during data processing can be an artifact of the instrumentation rather than the sample. For physical characterization of crystals, an experimental system and software have been developed to simultaneously measure the diffraction resolution and mosaic spread of macromolecular crystals. The contributions of the X-ray beam to the reflection angular widths were minimized by using a highly parallel, highly monochromatic synchrotron source. Hundreds of reflection profiles over a wide resolution range were rapidly measured using a charge-coupled device (CCD) area detector in combination with superfine φ-slicing data collection. The Lorentz effect and beam contributions were evaluated and deconvoluted from the recorded data. Data collection and processing is described. From 1° of superfine φ-slice data collected on a crystal of manganese superoxide dismutase, the mosaicities of 260 reflections were measured. The average mosaicity was 0.0101° (s.d. 0.0035°) measured as the full-width at half-maximum (FWHM) and ranged from 0.0011 to 0.0188°. Each reflection profile was individually fitted with two Gaussian profiles, with the first Gaussian contributing 55% (s.d. 9%) and the second contributing 35% (s.d. 9%) of the reflection. On average, the deconvoluted width of the first Gaussian was 0.0054° (s.d. 0.0015°) and the second was 0.0061° (s.d. 0.0023°). The mosaicity of the crystal was anisotropic, with FWHM values of 0.0068, 0.0140 and 0.0046° along the a,  b and c axes, respectively. The anisotropic mosaicity analysis indicates that the crystal is most perfect in the direction that corresponds to the favored growth direction of the crystal.
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    Crystallization and preliminary X-ray analyses of insect neurotoxins with analgesic effect from the scorpion Buthus martensii Karsch (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1012-1014 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Three insect neurotoxins from the scorpion Buthus martensii Karsch, named BmK I1, BmK I4 and BmK I6, have been purified and crystallized. BmK I1 and BmK I4 show strong toxicity to insects, while BmK I6 is relatively weaker. They all exhibit an evident analgesic effect on mice; this is a novel biological function for scorpion insect toxins. Their crystals diffract to at least 3.5 (BmK I1), 2.8 (BmK I4), 2.8 (BmK I6 crystal form I) and 2.2 Å (of BmK I6 crystal form II) resolution on an ordinary X-ray source. Crystals of BmK I1 belong to space group P6, with unit-cell parameters a = b = 66.2, c = 176.7 Å. BmK I4 crystallized in the tetragonal space group I4, with unit-cell parameters a = b = 134.5, c = 60.6 Å. BmK I6 has been crystallized in two forms: form I belongs to space group C2, with unit-cell parameters a = 46.5, b = 85.2, c = 32.6 Å, β = 110.5°; form II belongs to space group R3, with the hexagonal unit-cell parameters a = b = 44.5, c = 164.7 Å.
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    Crystallization and preliminary X-ray analysis of the Clostridium thermocellum cellulosome xylanase Z feruloyl esterase domain (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1027-1029 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Feruloyl esterases cleave ferulic acid from arabinoxylan and pectin. Feruloyl groups are believed to crosslink the polysaccharide chain within the polymer and to link hemicellulose to lignin, which may play a role in controlling the growth of plants. The Clostridium thermocellum cellulosome xylanase Z feruloyl esterase was expressed in Escherichia coli, purified and crystallized. The crystals diffract to 2.4 Å resolution and belong to the orthorhombic space group P212121, with unit-cell parameters a = 43.14, b = 63.77, c = 79.57 Å. Assuming one molecule per asymmetric unit, the Matthews coefficient is calculated to be 1.87 Å3 Da−1, which corresponds to a solvent content of 34%.
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    Crystallization and preliminary crystallographic analysis of the Rho-binding domain of bovine Rho-kinase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1042-1044 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Rho-kinase binds to a small GTPase Rho in a GTP-dependent manner and regulates many cytoskeletal events in the cell. The minimum region of bovine Rho-kinase sufficient for Rho-binding was expressed as a fusion protein with glutathione S-transferase. After removal of the glutathione S-transferase, thin plate crystals were obtained. The selenomethionine-substituted protein was introduced and crystallized, as was the native protein. The crystals of the Rho-binding domain of Rho-kinase belong to the space group C2, with unit-cell parameters a = 148.0 (2), b = 26.1 (1), c = 39.6 (1) Å, β = 90.3 (1)°. The crystals diffract to a resolution beyond 1.5 Å.
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    Crystallization and preliminary X-ray diffraction studies of d(ACGTAGCTACGT)2:[actinomycin D, (echinomycin)2] and d(ACGTAGCTACGT)2:[actinomycin D, (triostin A)2] complexes (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 344-347 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A DNA–multiple drug complex, d(ACGTAGCTACGT)2:[actinomycin D, (echinomycin)2] has been crystallized. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 85.6, b = 72.8, c = 56.6 Å, β = 101.5° at 93 K and Z = 8. The crystal diffracted to 3.0 Å resolution along the DNA fiber axis and to 3.5 Å resolution in other directions. The Patterson maps indicate that all complexes in the crystal are oriented along their helical axes in the [10\bar 1] direction.
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    Structural studies of MIP synthase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 348-350 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The conversion of glucose 6-phosphate to 1-L-myo-inositol 1-phosphate (MIP) by 1-L-myo-inositol 1-phosphate synthase (MIP synthase) is the first committed and rate-limiting step in the de novo biosynthesis of inositol in all eukaryotes. The importance of inositol-containing molecules both as membrane components and as critical second messenger signal-transduction species make the function and regulation of this enzyme important for a host of biologically important cellular functions including proliferation, neurostimulation, secretion and contraction. MIP synthase has been overexpressed in Esherichia coli and purified to homogeneity by chromatographic methods. Two crystal forms of MIP synthase were obtained by the hanging-drop vapor-diffusion method. Native data sets for both crystal forms were collected in-house on a Rigaku R-AXIS IIC imaging-plate detector. Crystal form I belongs to space group C2, with unit-cell parameters a = 153.0, b = 96.6, c = 122.6 Å, β = 126.4°, and diffracts to 2.5 Å resolution. Crystal form II belongs to space group P21, with unit-cell parameters a = 94.5, b = 186.2, c = 86.5 Å, β = 110.5°, and diffracts to 2.9 Å resolution.
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    Purification, crystallization and preliminary crystallographic studies of an integral membrane protein, cytochrome bo3 ubiquinol oxidase from Escherichia coli (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1076-1078 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cytochrome bo3 ubiquinol oxidase has been successfully purified for crystallization. Single crystals of this integral membrane protein diffract X-rays to 3.5 Å resolution and belong to the orthorhombic space group C2221. From the diffraction data, the unit-cell parameters were determined to be a = 91.3, b = 370.3, c = 232.4 Å. The crystals have a solvent content of 59% and contain two molecules per asymmetric unit. A search model generated from the structures of cytochrome c oxidase from Paracoccus denitrificans and the extrinsic domain of cytochrome bo3 ubiquinol oxidase from Escherichia coli was used for molecular-replacement studies, resulting in a solution with sensible molecular packing.
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    Structure of jack bean chitinase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1096-1099 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of jack bean chitinase was solved at 1.8 Å resolution by molecular replacement. It is an α-helical protein with three disulfide bridges. The active site is related in structure to animal and viral lysozymes. However, unlike in lysozyme, the architecture of the active site suggests a single-step cleavage. According to this mechanism, Glu68 is the proton donor and Glu90 assists in the reaction by moving towards the substrate and recruiting a water molecule that acts as the nucleophile. In this model, a water molecule was found in contact with Glu90 Oε1 and Thr119 Oγ at a distance of 3.0 and 2.8 Å, respectively. The model is in accordance with the observed inversion mechanism.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744490000857X
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  • 91
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    A flexible and efficient procedure for the solution and phase refinement of protein structures (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1137-1147 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An ab initio method is described for solving protein structures for which atomic resolution (better than 1.2 Å) data are available. The problem is divided into two stages. Firstly, a substructure composed of a small percentage (∼5%) of the scattering matter of the unit cell is positioned. This is used to generate a starting set of phases that are slightly better than random. Secondly, the full structure is developed from this phase set. The substructure can be a constellation of atoms that scatter anomalously, such as metal or S atoms. Alternatively, a structural fragment such as an idealized α-helix or a motif from some distantly related protein can be orientated and sometimes positioned by an extensive molecular-replacement search, checking the correlation coefficient between observed and calculated structure factors for the highest normalized structure-factor amplitudes |E|. The top solutions are further ranked on the correlation coefficient for all E values. The phases generated from such fragments are improved using Patterson superposition maps and Sayre-equation refinement carried out with fast Fourier transforms. Phase refinement is completed using a novel density-modification process referred to as dynamic density modification (DDM). The method is illustrated by the solution of a number of known proteins. It has proved fast and very effective, able in these tests to solve proteins of up to 5000 atoms. The resulting electron-density maps show the major part of the structures at atomic resolution and can readily be interpreted by automated procedures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744490000932X
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  • 92
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    Crystallization and preliminary X-ray diffraction analysis of a cytochrome P450 (CYP119) from Sulfolobus solfataricus (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1173-1175 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: CYP119 is a cytochrome P450 with a molecular weight of 43 kDa which has been isolated from the thermophilic archaeon Sulfolobus solfataricus. This enzyme is extremely stable to high temperature and high pressure. The first crystallization and preliminary crystallographic study of CYP119 is reported here. Crystals of CYP119 were obtained by the sitting-drop vapour-diffusion method using a precipitant solution containing 20%(w/v) PEG 4000 and 0.2 M sodium thiocyanate at pH 6.4. Using synchrotron radiation, the CYP119 crystal diffracted to 1.84 Å resolution. It belongs to the tetragonal space group P43212, with unit-cell parameters a = b = 86.17 (0.07), c = 221.11 (0.04) Å, in which the numbers in parentheses describe the standard deviations. Assuming two molecules of the CYP119 per asymmetric unit, the calculated molar volume (Vm) is 2.38 Å3 Da−1. Bijvoet and dispersive anomalous difference Patterson maps show a clear peak corresponding to the haem irons. The complete crystallographically defined structure is currently in progress using MIR (multiple isomorphous replacement) and MAD (multiwavelength anomalous diffraction) techniques.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900008234
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  • 93
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    Purification, crystallization and preliminary crystallographic data for rat cytosolic selenocysteine 498 to cysteine mutant thioredoxin reductase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1191-1193 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mammalian cytosolic thioredoxin reductase is a homodimer of 55 kDa subunit containing an essential penultimate selenocysteine residue. An active analogue of the rat enzyme in which cysteine replaces selenocysteine has been expressed in Escherichia coli cells at high levels and purified to homogeneity. The pure enzyme contains one FAD per subunit and shows spectral properties identical to that of the wild-type thioredoxin reductase. The isolated enzyme in its oxidized and reduced forms or the enzyme complexed with NADP+ was crystallized by the hanging-drop vapour-diffusion method. The diffraction pattern extends to 3 Å resolution. The crystals are monoclinic, space group P21, with unit-cell parameters a = 78.9, b = 140.5, c = 170.8 Å, α = 94.6°. There are three dimeric molecules in the asymmetric unit.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900009458
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  • 94
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    Crystallization and preliminary X-ray crystallographic analysis of water channel AQP1 (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1198-1200 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Aquaporin-1 (AQP1), a water channel from bovine red blood cells has been deglycosylated, purified to homogeneity and crystallized in a form suitable for X-ray crystallographic study. Crystals are grown using polyethylene glycol as precipitant and belong to the tetragonal space group I422, with unit-cell parameters a = b = 93.4, c = 180.4 Å. The crystals diffract beyond 2.2 Å resolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900008143
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  • 95
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    Direct methods and protein crystallography at low resolution (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1205-1214 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The tools of modern direct methods are examined and their limitations for solving protein structures discussed. Direct methods need atomic resolution data (1.1–1.2 Å) for structures of around 1000 atoms if no heavy atom is present. For low-resolution data, alternative approaches are necessary and these include maximum entropy, symbolic addition, Sayre's equation, group scattering factors and electron microscopy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900009355
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  • 96
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    Density constraints and low-resolution phasing (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1233-1244 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Direct phasing needs additional information of a non-specific kind in order to select the correct phase set from all possible ones. This paper analyses the use of constraints which can be formulated in terms of electron-density values. One- and multi-dimensional histograms and connectivity properties are implemented as such constraints in density-modification procedures. These approaches usually cannot unambiguously select the best solution from a set of alternative phase variants. Nevertheless, they do allow the rejection of wrong solutions and the use of cluster analysis and averaging on the remaining variants provide a good starting point for further phase-refinement procedures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900009331
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  • 97
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    Structural analysis of non-crystalline macromolecules: the ribosome (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1253-1258 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Single-particle analysis using cryo-electron microscopy has emerged recently as a tool for elucidating the structure of biological macromolecules and their assemblies. A prerequisite for single-particle analysis is an ensemble of images of structurally identical particles in different orientations. There are a variety of techniques used for image processing of this type of object in electron microscopy. The paper gives an overview of the general philosophy of image analysis of single particles in electron microscopy. It has been shown that multivariate statistical analysis of large data sets in conjunction with angular reconstitution is capable of yielding a structural resolution approaching that of X-ray structural analysis of large macromolecules. Structure preservation during specimen preparation for electron microscopy is crucial for high-resolution studies. Nowadays, cryo-electron microscopy is a beneficial method for studying biological macromolecules in their natural environment, allowing their rapid freezing in a particular functional state. The processing of images of 50S Escherichia coli ribosomal subunits embedded in vitreous ice is used as an example of image analysis of single particles at 7.5 Å resolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744490001115X
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  • 98
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    Low-resolution phasing (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1-1 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900010155
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  • 99
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    Improving the X-ray resolution by reversible flash-cooling combined with concentration screening, as exemplified with PPase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 595-603 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A significant improvement in the X-ray resolution of crystals of Escherichia coli inorganic pyrophosphatase at cryotemperature was obtained as a result of studying the relationship between the crystal order and cryosolution component concentrations. To perform the experiments, the ability to reverse the flash-cooling process and to return a crystal to ambient temperature was used. In each cycle, the crystal was transferred from a cold nitrogen-gas stream to a cryosolution with modified concentrations of the components. The crystal was then flash-cooled again and the diffraction quality checked. Such a technique allows the screening of a wide concentration range rather quickly without using a large number of crystals and allows the determination of optimal cryosolution component concentrations. The resolution limit for crystals of pyrophosphatase increased by almost 0.7 Å, from 1.8 to 1.15 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900002493
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  • 100
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    The use of wavelet transforms in low-resolution phase extension (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 625-633 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A method to extend low-resolution phases has been developed using histogram matching not only of the electron density itself but also of histograms obtained from the different levels of detail provided by the wavelet transform of the electron density. It is shown that the method can extend phases from 10 Å to around 6–7 Å on a wide range of trial structures differing in size, space group and solvent content. This level of phase extension can improve the electron-density map from little more than a molecular envelope to one in which secondary structure can often be identified.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900003103
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