J. Vicat

Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 Å resolution

The crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici has been determined at a resolution of 1.84 A and refined to an R-factor of 0.169. Crystals belong to space group P4(3)2(1)2 with unit cell dimensions a = b = 34.44 A and c = 74.78 A. The structure was determined by molecular replacement using the previously published model of an homologous ferredoxin and refined by molecular dynamics techniques. The model contains the protein and 46 water molecules. Only two amino acid residues, Asp27 and Asp28, are poorly defined in the electron density maps. The molecule has an overall chain fold similar to that of other [4Fe-4S] bacterial ferredoxins of known structure. The two [4Fe-4S] clusters display similar bond distances and angles. In both of them the co-ordination of one iron atom (bound to Cys11 and Cys40) is slightly distorted as compared with that of the other iron atoms. A core of hydrophobic residues and a few water molecules contribute to the stability of the structure. The [4Fe-4S] clusters interact with the polypeptide chain through eight hydrogen bonds each, in addition to the covalent Fe-Scys bonds. The ferredoxin from Clostridium acidurici is the most typical clostridial ferredoxin crystallized so far and the biological implications of the newly determined structure are discussed.

Gd-HPDO3A, a complex to obtain high-phasing-power heavy-atom derivatives for SAD and MAD experiments: results with tetragonal hen egg-white lysozyme

A neutral gadolinium complex, Gd-HPDO3A, is shown to be a good candidate to use to obtain heavy-atom derivatives and solve macromolecular structures using anomalous dispersion. Tetragonal crystals of a gadolinium derivative of hen egg-white lysozyme were obtained by co-crystallization using different concentrations of the complex. Diffraction data from three derivative crystals (100, 50 and 10 mM) were collected to a resolution of 1.7 A using Cu Kalpha radiation from a rotating anode. Two strong binding sites of the gadolinium complex to the protein were located from the gadolinium anomalous signal in both the 100 and 50 mM derivatives. A single site is occupied in the 10 mM derivative. Phasing using the anomalous signal at a single wavelength (SAD method) leads to an electron-density map of high quality. The structure of the 100 mM derivative has been refined. Two molecules of the gadolinium complex are close together. Both molecules are located close to tryptophan residues. Four chloride ions were found. The exceptional quality of the SAD electron-density map, only enhanced by solvent flattening, suggests that single-wavelength anomalous scattering with the Gd-HPDO3A complex may be sufficient to solve protein structures of high molecular weight by synchrotron-radiation experiments, if not by laboratory experiments.

Mise en evidence et etude de la phase ordonnée Y2Hf7O17 dans le système HfO2Y2O3

Resume Le systeme HfO2Y2O3 presente une phase ordonnee par rapport a la phase metastable type fluorite, correspondant au compose defini Y2Hf7O17. La transformation ordre → desordre a eteetudiee par differentes methodes. Les resultats obtenus permettent de tracer le diagramme de phase du systeme HfO2Y2O3 dans la zone riche en dioxyde de hafnium.

Thermal and physical properties of hollandite-type K1.3Mn8O16 and (K,H3O)xMn8O16

Abstract Two kinds of samples of cryptomelane: synthetic single crystals of K 1.33 Mn 8 O 16 (A) and (K,H 3 O) x Mn 8 O 16 powder prepared by aqueous chemistry (B) were studied by thermogravimetry, magnetic, and electrical (dc and ac) measurements. B loses water at 100–185°C. A and B are decomposed in the range 460–610°C into Mn 2 O 3 in air and MnO, under vacuum. They are antiferromagnetic with T N 18 K (A), 11 K (B). A is a semiconductor with σ(300 K) ∼ 3 Ω −1 m −1 and E σ = 0.38 eV. The ac measurements did not reveal any significant contribution of ionic conduction up to 740 K.

A new class of gadolinium complexes employed to obtain high-phasing-power heavy-atom derivatives: results from SAD experiments with hen egg-white lysozyme and urate oxidase from Aspergillus flavus.

Seven gadolinium complexes are shown to be excellent compounds for the preparation of heavy-atom derivatives for macromolecular crystallography projects. De novo phasing has been carried out using single-wavelength anomalous diffraction (SAD) on a series of gadolinium-derivative crystals of two proteins: hen egg-white lysozyme and urate oxidase from Aspergillus flavus. Lysozyme derivative crystals were obtained by co-crystallizing the protein with the corresponding gadolinium complex at a concentration of 100 mM. Diffraction data were collected to a resolution of 1.7 A using Cu K(alpha) radiation from a rotating-anode generator, making use of the high anomalous signal of gadolinium at this wavelength. Urate oxidase derivative crystals were obtained by soaking native crystals in 100 mM gadolinium complex solutions. Diffraction data were collected to a resolution close to 3 A using X-rays at the Gd L(III) absorption edge, taking advantage of the sharp white line on that edge. For all urate oxidase derivative crystals and three of the lysozyme crystals, SAD phasing led to electron-density maps of very high quality, allowing unambiguous chain tracing. From this study, the binding effectiveness of the gadolinium complexes seems to be related to the nature of the precipitant used for crystallization. These gadolinium complexes represent a new class of high-phasing-power heavy-atom derivatives that may be used for high-throughput structure-determination projects.

X-ray spectroscopy and X-ray diffraction at wavelengths near the K-absorption edge of phosphorus

Phosphorus is an abundant element in living organisms. It is traceable by its X-ray absorption spectrum which shows a strong white line at its K-edge, comparable with that observed for the L(III) edges of rare earth ions. With purple membrane, the variation of the imaginary part of the anomalous dispersion of phosphorus is found to be close to 20 anomalous electron units. Anomalous diffraction experiments at wavelengths near the K-absorption edge of phosphorus confirm this result. The spatial distribution of lipids derived from anomalous diffraction agrees with earlier results from neutron diffraction. Test experiments on single crystals of the carrier protein using 5.76 A photons gave a first low-resolution diffraction pattern. Various techniques of crystal mounting were attempted. In addition, fluorescence measurements on a solution of threonine synthase appear to hint at a change of the phosphate environment of the cofactor upon activator binding.

Feasibility and review of anomalous X-ray diffraction at long wavelengths in materials research and protein crystallography

The feasibility and a review of progress in the long-wavelengths anomalous dispersion technique is given in the context of the development of beamline ID1 of the ESRF for such studies. First experiments on this beamline and their analyses are described. The first study reports on the use of uranium which exhibits an unusually strong anomalous dispersion at its M(V) absorption edge (lambda(M(V)) = 3.5 A). The anomalous scattering amplitude of uranium with 110 anomalous electrons exceeds the resonance scattering of other strong anomalous scatterers like that of the rare earth ions by a factor of four. The resulting exceptional phasing power of uranium is most attractive in protein crystallography using the MAD method. The anomalous dispersion of a uranium derivative of asparaginyl-tRNA synthetase (hexagonal, a = 124.4 A, c = 123.4 A) has been measured at three wavelengths near the M(V) edge using beamline ID1 of the ESRF. The present set-up allowed the measurement of 10% of the possible reflections at a resolution of 8 A. This is mainly due to the low sensitivity of the CCD camera. The second study, involving DAFS experiments at wavelengths near the K-absorption edge of chlorine (lambda(K) = 4.4 A), reports the use of salt crystals which give rise to much stronger intensities of diffraction peaks than those of protein crystals. In the case of a crystal of pentamethylammonium undecachlorodibismuthate (PMACB, orthorhombic, a = 13.00 A, b = 14.038 A, c = 15.45 A), all reflections within the resolution range from 6.4 A to 3.5 A and the total scan width of 24 degrees were collected. The crystalline structure of PMACB implies two chemically distinct states of the Cl atom. Consequently, different dispersions near the K-edge of chlorine are expected. The dispersion of the intensity of five Bragg peaks of the PMACB crystal has been measured at 30 wavelengths. The relative success of these preliminary experiments with X-rays of long wavelength shows that the measurement of anomalous X-ray diffraction at wavelengths beyond 3 A is feasible. Starting from the experience gained in these experiments, an increased efficiency of the instrument ID1 by two to three orders of magnitude will be achieved in this wavelength range. A comparison with different techniques of anomalous diffraction which rely on the use of argon/ethane-filled multiwire chambers and image plates as detectors for wavelengths near the K-edge of sulfur and phosphorus is also given.

Exploration of the supramolecular interactions involving tris-dipicolinate lanthanide complexes in protein crystals by a combined biostructural, computational and NMR study

Incorporating in a non-covalent manner lanthanide derivatives into protein crystals has shown to be of prime interest for X-ray crystallography, insofar as these versatile compounds can co-crystallize with proteins through supramolecular interactions, in addition to being strong anomalous scatterers for anomalous-based diffraction techniques. In this paper, the selective affinity of tris-dipicolinate lanthanide complexes for cationic amino-acid residues is explored, using a panel of experimental (X-ray diffraction, NMR titration) and theoretical methods that provides access to an accurate description of the interaction process.

Heavy‐atom derivatives in lipidic cubic phases: results on hen egg‐white lysozyme tetragonal derivative crystals with Gd‐HPDO3A complex

Gd-HPDO3A, a neutral gadolinium complex, is a good candidate for obtaining heavy-atom-derivative crystals by the lipidic cubic phase crystallization method known to be effective for membrane proteins. Gadolinium-derivative crystals of hen egg-white lysozyme were obtained by co-crystallizing the protein with 100 mM Gd-HPDO3A in a monoolein cubic phase. Diffraction data were collected to a resolution of 1.7 A using Cu Kalpha radiation from a rotating-anode generator. Two binding sites of the gadolinium complex were located from the strong gadolinium anomalous signal. The Gd-atom positions and their refined occupancies were found to be identical to those found in derivative crystals of hen egg-white lysozyme obtained by co-crystallizing the protein with 100 mM Gd-HPDO3A using the hanging-drop technique. Moreover, the refined structures are isomorphous. The lipidic cubic phase is not disturbed by the high concentration of Gd-HPDO3A. This experiment demonstrates that a gadolinium complex, Gd-HPDO3A, can be used to obtain derivative crystals by the lipidic cubic phase crystallization method. Further studies with membrane proteins that are known to crystallize in lipidic cubic phases will be undertaken with Gd-HPDO3A and other Gd complexes to test whether derivative crystals with high Gd-site occupancies can be obtained.

A new lanthanide complex for protein structure determination using anomalous diffraction

Despite the enormous success of cryocrystallographic techniques, there has been surprisingly little understanding of the fundamental mechanisms relevant to their successful application. I will describe a variety of experiments designed to provide a quantitative, rational basis for cryoprotection and flash cooling [1]. These experiments have resulted in a new approach to cryopreserving protein crystals. Both the cryoprotectant concentrations required to inhibit hexagonal ice formation and the mosaicities of frozen crystals are dramatically reduced over current best practices, simplifying cryoprotectant screening and yielding higher resolution structural information. At the same time, there are many excellent reasons to collect diffraction data at room temperature. Room temperature screening can diagnose problems in as-grown crystal order and in cryoprotective procedures, allowing problem crystals to be weeded out early in the diffraction pipeline. Room temperature may also yield higher resolution structures that more faithfully represent the biologically relevant conformation. I will describe a simple technology [2] that makes room temperature data collection as easy as at low temperatures, and that can be implemented in a high-throughput environment.