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  • 1
    Electronic Resource
    Electronic Resource
    Vanadium K-edge x-ray absorption spectroscopy of bromoperoxidase from Ascophyllum nodosum (1989)
    s.l. : American Chemical Society
    Biochemistry 28 (1989), S. 7968-7973 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00445a062
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  • 2
    Electronic Resource
    Electronic Resource
    An understanding of the x-ray absorption near-edge structure of copper(II) imidazole complexes (1990)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 112 (1990), S. 4265-4268 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00167a022
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  • 3
    Electronic Resource
    Electronic Resource
    EXAFS studies on pig plasma amine oxidase. A detailed structural analysis using the curved wave multiple scattering approach (1989)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 111 (1989), S. 102-107 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00183a018
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  • 4
    Electronic Resource
    Electronic Resource
    The mechanism of iron uptake by transferrins: the structure of an 18 kDa NII-domain fragment from duck ovotransferrin at 2.3 Å resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 292-304 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular structure of an iron-containing 18 kDa fragment of duck ovotransferrin, obtained by proteolysis of the intact protein, has been elucidated by protein crystallographic techniques at 2.3 Å resolution. This structure supports a mechanism of iron uptake in the intact protein whereby the binding of the synergistic (bi)carbonate anion is followed by binding of the metal with the lobe in the open configuration. These stages are then followed by domain closure in which the aspartic acid residue plays a further key role, by forming an interdomain hydrogen-bond interaction in addition to serving as a ligand to the iron. This essential dual role is highlighted by model building studies on the C-terminal lobe of a known human variant. In this variant a mutation of a glycine by an arginine residue enables the aspartic acid to form an ion pair and reduce its effectiveness for both metal binding and domain closure. The X-ray structure of the 18 kDa fragment strongly suggests that the histidine residue present at the iron binding site of the intact protein and arising from the second interdomain connecting strand has been removed during the preparative proteolysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992012101
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  • 5
    Electronic Resource
    Electronic Resource
    Direct-Method Structure Determination of the Native Azurin II Protein Using One-Wavelength Anomalous Scattering Data (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 937-941 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The one-wavelength anomalous scattering (OAS) X-ray diffraction data of azurin II, a copper-containing protein from Alcaligenes xylosoxidans were collected at the Photon Factory, Japan at a `routine' wavelength of 0.97 Å. The structure had been originally solved by the molecular-replacement method [Dodd, Hasnain, Abraham, Eady & Smith (1995). Acta Cryst. D51, 1052–1064]. As a technique of ab initio structure determination, the direct method [Fan, Hao, Gu, Qian, Zheng & Ke (1990). Acta Cryst. A46, 935–939] was attempted to break the phase ambiguity intrinsic to OAS data. The phases were then improved using the solvent-flattening method. The final electron-density map clearly shows most Cα positions and many side chains and it is traceable without prior knowledge of the structure. It is concluded that the direct method is capable of phasing anomalous scattering data collected at one wavelength from moderate-sized native proteins (Mw ∼ 20 kDa) which contain copper or atoms with a similar scattering power.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996003939
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  • 6
    Electronic Resource
    Electronic Resource
    Structures of a Blue-Copper Nitrite Reductase and its Substrate-Bound Complex (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 406-418 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Copper-containing nitrite reductases (NiR's) have been conveniently subdivided into blue and green NiR's which are thought to be redox partners of azurins and pseudo-azurins, respectively. Crystal structures of two green NiR's have recently been determined. Alcaligenes xylosoxidans has been shown to have a blue-copper nitrite reductase (AxNiR) and two azurins with 67% homology both of which donate electrons to it effectively. The first crystal structure of a blue NiR (AxNiR) in its oxidized and nitrite-bound forms, with particular emphasis to the Cu sites, is presented. The Cu-Smet distance is the same as those in the green NiR's. Thus, the length of this interaction is unlikely to be responsible for differences in colour. Crystallographic data presented here taken together with structural data of other single Cu type-1 proteins and their mutants suggest that the displacement of Cu from the strong ligand plane is perhaps the cause for the differences in colour observed for otherwise `classical' blue Cu centre. Nitrite is observed binding to the catalytic Cu in a bidentate fashion displacing the water molecule, offering a neat rationalization for the XAFS observation that the type-2 Cu-ligand distances increase on nitrite binding as a result of increased coordination. These results are discussed in terms of enzyme mechanism.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997002667
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  • 7
    Electronic Resource
    Electronic Resource
    Ab initio phasing using molecular envelope from solution X-ray scattering (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 243-246 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Solving the phase problem is the crucial and quite often the most difficult and time-consuming step in crystallographic structure determination. The traditional methods of isomorphous replacement (MIR or SIR) and molecular replacement require the availability of an isomorphous heavy-atom derivative or the structure of a homologous protein, respectively. Here, a method is presented which utilizes the low-resolution molecular shape determined from solution X-ray scattering data for the molecular search. The molecular shape of a protein is an important structural property and can be determined directly by the small-angle scattering technique. The idea of locating this molecular shape in the crystallographic unit cell has been tested with experimental diffraction data from nitrite reductase (NiR). The conventional Patterson search proved to be unsuccessful, as the intra-envelope vectors are uniformly distributed and do not match those of intra-molecular (atom-to-atom) vectors. A direct real-space search for orientation and translation was then performed. A self-rotation function using 2.8 Å crystallographic data yielded the polar angles of the non-crystallographic threefold axis. Knowledge of the orientation of this axis reduces the potential six-dimensional search to four (Eulerian angle γ and three translational parameters). The direct four-dimensional search within the unit cell produced a clear solution. The electron-density map based on this solution agrees well with the known structure, and the phase error calculated from the map was 61° within 20 Å resolution. It is anticipated that the low-resolution envelope can be used as a starting model for phase extension by the maximum-entropy and density-modification method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998011342
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  • 8
    Electronic Resource
    Electronic Resource
    Is single-wavelength anomalous scattering sufficient for solving phases? A comparison of different methods for a 2.1 Å structure solution (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1620-1622 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of rusticyanin is the largest unknown structure (Mr = 16.8 kDa) which has been recently solved by the direct-methods approach using only single-wavelength anomalous scattering (SAS) data from the native protein [Harvey et al. (1998). Acta Cryst. D54, 629–635]. Here, the results of the Sim distribution approach [Hendrickson & Teeter (1981). Nature (London), 290, 107–113] and of the CCP4 procedure MLPHARE [Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763] are compared with those from direct methods. Analysis against the final refined model shows that direct methods produced significantly better phases (average phase error 56°) and therefore significantly better electron-density maps than the Sim distribution and MLPHARE approaches (average phase error was around 63° in both cases).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999007726
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  • 9
    Electronic Resource
    Electronic Resource
    Structure of a new azurin from the denitrifying bacterium Alcaligenes xylosoxidans at high resolution (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 1052-1064 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: It has been reported previously that Alcaligenes xylosoxidans (NC1MB 11015) grown under denitrifying conditions produces two azurins instead of the single previously identified azurin [Dodd, Hasnain, Hunter, Abraham, Debenham, Kanzler, Eldridge, Eady, Ambler & Smith (1995). Biochemistry. In the press]. The new azurin, called azurin II, has been crystallized as blue elongated rectangular prisms with the tetragonal space group P4122 and unit-cell parameters a = b = 52.65, c = 100.63 Å. X-ray crystallographic data extending to 1.9 Å resolution were collected by the Weissenberg method using 200 × 400 mm image plates and synchrotron X-rays of wavelength 0.97 Å. The three-dimensional structure of azurin II has been solved by the molecular-replacement method using the structure of azurin from Alcaligenes denitrificans NCTC 8582 with which this new azurin shows a close homology. The quality of the initial map was sufficient to predict a number of sequence differences. The model is currently refined to an R-factor of 18.8% with X-ray data between 8.5 and 1.9 Å. The final model of 961 protein atoms, one Cu atom and 50 water molecules has r.m.s. deviations from ideality of 0.009 Å for bond lengths and 1.7° for bond angles. The overall structure is similar to that of the azurin from A. denitrificans NCTC 8582. It has a β-barrel structure with the Cu atom located near the top end of the molecule. The Cu atom is coordinated to Nδ of His46 and His117 at 2.02 Å and to Sγ of Cys112 at 2.12 Å, while the carbonyl O atom of Gly45 and Sδ atom of Met121 provide the additional interactions at 2.75 and 3.26 Å, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995007554
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  • 10
    Electronic Resource
    Electronic Resource
    Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1002-1006 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Solution of the phase problem is central to crystallographic structure determination. The conventional methods of isomorphous replacement (MIR or SIR) and molecular replacement are ineffective in the absence of a suitable isomorphous heavy-atom derivative or knowledge of the structure of a homologous protein. A recent method utilizing the low-resolution molecular shape determined from solution X-ray scattering data has shown to be successful in locating the molecular shape within the crystallographic unit cell in the case of the trimer nitrite reductase (NiR, 105 kDa) [Hao et al. (1999), Acta Cryst. D55, 243–246]. This was achieved by performing a direct real-space search for orientation and translation using knowledge of the orientation of the polar angles of the non-crystallographic axis obtained by performing a self-rotation on crystallographic data. This effectively reduces the potential six-dimensional search to a four-dimensional one (Eulerian angle γ and three translational parameters). In the case of NiR, the direct four-dimensional search produced a clear solution that was in good agreement with the known structure. The program FSEARCH incorporating this method has been generalized to handle molecules from all space groups and in particular those in possession of non-crystallographic symmetry. However, the method employed was initially unsuccessful when applied to the small dimeric molecule superoxide dismutase (SOD, 32 kDa) owing to the absence of strong reflections at low resolution caused by saturation at the detector. The determined solution deviated greatly from that of the known structure [Hough & Hasnain (1999), J. Mol. Biol. 287, 579–592]. It was found that once these absent reflections were replaced by a series of randomly generated intensity values and cluster analysis was performed on the output, the signal-to-noise ratio was improved and a most probable solution was found. The electron-density map of the stochastically determined solution agrees well with the known structure; the phase error calculated from this map was 67° within 14 Å resolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900007721
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