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Bicheng Wang - One of the best experts on this subject based on the ideXlab platform.

  • displacement of iron by zinc at the diiron site of desulfovibrio vulgaris rubrerythrin x ray crystal structure and Anomalous Scattering analysis
    Journal of Inorganic Biochemistry, 2004
    Co-Authors: Shi Jin, Donald M Kurtz, Zhijie Liu, John P Rose, Bicheng Wang
    Abstract:

    Abstract X-ray crystal structures of recombinant Desulfovibrio ( D. ) vulgaris rubrerythrin (Rbr) have shown a diiron site, whereas the crystal structure of Rbr “as-isolated” from D. vulgaris was reported to contain a mixed Zn,Fe binuclear site. To investigate the possibility that zinc had displaced iron during isolation or crystallization of the “as-isolated” D. vulgaris Rbr, the X-ray crystal structure of recombinant D. vulgaris all-iron Rbr that had been incubated with excess zinc sulfate prior to crystallization, yielding a protein labeled Zn,FeRbr, was solved. Analysis of the Anomalous Scattering data obtained at two different wavelengths showed that zinc had displaced a significant proportion of iron from both iron centers of the diiron site, and that no iron had been displaced from the [Fe(SCys) 4 ] site. UV–visible absorption spectra of the redissolved Zn,FeRbr crystals showed 30–40% retention of oxo-bridged diferric sites, and the redissolved crystals had 37% of the peroxidase specific activity of the starting all-iron Rbr, which, together with the crystallographic results, indicate a predominant mixture of Fe1,Fe2 and Zn1,Zn2 sites. The structure of the Zn(Fe)1,Fe(Zn)2 binuclear site in the Zn,FeRbr crystals was very similar to that of the Zn,Fe binuclear site reported for the “as-isolated” D. vulgaris Rbr, including tetrahedral four-coordination at the Zn(Fe)1 site. The diiron sites in the recombinant Zn,FeRbr crystals were likely at least partially reduced during synchrotron irradiation. Our results suggest that the mixed-metal binuclear site reported for the “as-isolated” D. vulgaris Rbr could be due to displacement of iron from a native diiron site by adventitious zinc during isolation and/or crystallization, and that reduced diiron and dizinc sites can adopt very similar structures in Rbr.

  • structure of the ca2 regulated photoprotein obelin at 1 7 a resolution determined directly from its sulfur substructure
    Protein Science, 2000
    Co-Authors: Zhijie Liu, John P Rose, Eugene S Vysotski, Chunjung Chen, John Lee, Bicheng Wang
    Abstract:

    The crystal structure of the photoprotein obelin (22.2 kDa) from Obelia longissima has been determined and refined to 1.7 A resolution. Contrary to the prediction of a peroxide, the noncovalently bound substrate, coelenterazine, has only a single oxygen atom bound at the C2-position. The protein-coelenterazine 2-oxy complex observed in the crystals is photo-active because, in the presence of calcium ion, bioluminescence emission within the crystal is observed. This structure represents only the second de novo protein structure determined using the Anomalous Scattering signal of the sulfur substructure in the crystal. The method used here is theoretically different from that used for crambin in 1981 (4.72 kDa) and represents a significant advancement in protein crystal structure determination.

  • crystal structure of a bovine neurophysin ii dipeptide complex at 2 8 a determined from the single wavelength Anomalous Scattering signal of an incorporated iodine atom
    Proceedings of the National Academy of Sciences of the United States of America, 1991
    Co-Authors: Liqing Chen, John Rose, Esther Breslow, Daniel S C Yang, Wenrui Chang, William Furey, Martin Sax, Bicheng Wang
    Abstract:

    Abstract The crystal structure of a dipeptide complex of bovine neurophysin II has been solved at 2.8 A resolution solely by using single-wavelength Anomalous Scattering data from a single iodinated derivative. The asymmetric unit is an elongated tetramer of dimensions 110 x 40 x 30 A, composed of two dimers related by pseudo twofold symmetry. Each monomer consists of two homologous layers, each with four antiparallel beta-strands. The two regions are connected by a helix followed by a long loop. Monomer-monomer contacts involve antiparallel beta-sheet interactions, which form a dimer with two layers of eight beta-strands. One peptide per monomer occupies the principal hormone-binding pocket formed by part of the amino-terminal region and parts of the connecting helix and loop, with binding to protein consistent with conclusions drawn from solution studies. Dimer-dimer contacts involve the Tyr49 region adjacent to this site. A fifth dipeptide, of unknown biological significance, helps to stabilize one of the monomer-monomer interfaces and the tetramer-tetramer network in the crystal.

G.d. Smith - One of the best experts on this subject based on the ideXlab platform.

Quan Hao - One of the best experts on this subject based on the ideXlab platform.

  • J. Synchrotron Rad. (2000). 7, 148±151 Direct phasing of one-wavelength Anomalous-Scattering data
    2015
    Co-Authors: Quan Hao
    Abstract:

    This paper presents a brief survey of methods in ab initio phasing of one-wavelength Anomalous-Scattering data. In particular, the method implemented in the computer program OASIS has been tested using two new data sets from orotidine 50-monophosphate decarboxylase (OMPDC) [Appleby et al. (2000). Proc. Natl Acad. Sci. USA. In the press] and PurE [Mathews et al. (1999). Structure, 7(11), 1395±1406]. The Se atoms were located by the small-molecule program SAPI. The electron density maps after OASIS and density modi®cation for both structures clearly revealed the C trace and, in the case of PurE, most side-chains. The test with the OMPDC data demonstrated that, by exploiting the Anomalous signal at a single wavelength, direct methods can be used to determine phases at moderate (2.5 AÊ) macromolecular crystallographic resolution for a large-size protein (5663 non-H atoms in the asymmetric unit). The exceptionally good quality of the electron map shown in the case of PurE suggested that fully automatic model ®tting is possible

  • oasis a computer program for breaking phase ambiguity in one wavelength Anomalous Scattering or single isomorphous substitution replacement data
    Journal of Applied Crystallography, 2000
    Co-Authors: Quan Hao, C D Zheng, H F Fan
    Abstract:

    The phase problem is reduced to a sign problem once the Anomalous-scatterer or the replacing-heavy-atom sites are located. OASIS adopts the CCP4 format [Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763]. It applies a direct-method procedure to break the phase ambiguity intrinsic to one-wavelength Anomalous Scattering (OAS) or single isomorphous replacement (SIR) data.

Su Xiao-dong - One of the best experts on this subject based on the ideXlab platform.

  • Get Phases from Arsenic Anomalous Scattering: de novo SAD Phasing of Two Protein Structures Crystallized in Cacodylate Buffer
    plos one, 2011
    Co-Authors: Liu Xiang, Zhang Heng, Wang Xiao-jun, Li Lan-fen, Su Xiao-dong
    Abstract:

    The crystal structures of two proteins, a putative pyrazinamidase/nicotinamidase from the dental pathogen Streptococcus mutans (SmPncA) and the human caspase-6 (Casp6), were solved by de novo arsenic single-wavelength Anomalous diffraction (As-SAD) phasing method. Arsenic (As), an uncommonly used element in SAD phasing, was covalently introduced into proteins by cacodylic acid, the buffering agent in the crystallization reservoirs. In SmPncA, the only cysteine was bound to dimethylarsinoyl, which is a pentavalent arsenic group (As (V)). This arsenic atom and a protein-bound zinc atom both generated Anomalous signals. The predominant contribution, however, was from the As Anomalous signals, which were sufficient to phase the SmPncA structure alone. In Casp6, four cysteines were found to bind cacodyl, a trivalent arsenic group (As (III)), in the presence of the reducing agent, dithiothreitol (DTT), and arsenic atoms were the only Anomalous scatterers for SAD phasing. Analyses and discussion of these two As-SAD phasing examples and comparison of As with other traditional heavy atoms that generate Anomalous signals, together with a few arsenic-based de novo phasing cases reported previously strongly suggest that As is an ideal Anomalous scatterer for SAD phasing in protein crystallography.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000294686100025&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Multidisciplinary SciencesSCI(E)PubMed6ARTICLE9e24227

Navraj S Pannu - One of the best experts on this subject based on the ideXlab platform.

  • automatic protein structure solution from weak x ray data
    Nature Communications, 2013
    Co-Authors: Pavol Skubak, Navraj S Pannu
    Abstract:

    X-ray crystallography is a routine technique used to solve protein structures, but is often limited by weak Anomalous Scattering signals and low-resolution data. Here, the authors develop a synergistic algorithm to significantly increase the success rate of structure solution when the signal is weak.

  • a multivariate likelihood siras function for phasing and model refinement
    Acta Crystallographica Section D-biological Crystallography, 2009
    Co-Authors: Pavol Skubak, Garib N Murshudov, Navraj S Pannu
    Abstract:

    A likelihood function based on the multivariate probability distribution of all observed structure-factor amplitudes from a single isomorphous replacement with Anomalous Scattering experiment has been derived and implemented for use in substructure refinement and phasing as well as macromolecular model refinement. Efficient calculation of a multidimensional integration required for function evaluation has been achieved by approximations based on the function's properties. The use of the function in both phasing and protein model building with iterative refinement was essential for successful automated model building in the test cases presented.