Phasing from an envelope.
TL;DR: A recent method utilizing the low-resolution molecular shape determined from solution X-ray scattering data has been shown to be successful in locating the molecular shape within the crystallographic unit cell for the cases of the trimeric nitrite reductase and the dimeric superoxide dismutase.
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Abstract: Solution of the phase problem is central to crystallographic structure determination. Conventional molecular-replacement methods are ineffective in the absence of 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 been shown to be successful in locating the molecular shape within the crystallographic unit cell for the cases of the trimeric nitrite reductase (AxNiR, 105 kDa) and the dimeric superoxide dismutase (SOD, 32 kDa). This was achieved by performing a direct real-space search for orientation and translation using the orientation of the non-crystallographic axis obtained by performing a self-rotation on the crystallographic data. This effectively reduces the potential six-dimensional search to a four-dimensional one (Eulerian angle γ and three translational parameters). The program FSEARCH incorporating this method has been generalized to handle molecules from all space groups. The program can also be used in general six-dimensional cases for a molecular-replacement solution given a predetermined envelope from any source, such as electron-microscopic images or solution scattering, provided that the envelope can be converted to the standard CCP4 map format or expressed in terms of spherical harmonics. It is hoped that this method will greatly facilitate the ab initio structure determination of proteins and provide a good foundation for further structure refinement.
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Citations
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
TL;DR: In this article, a review of the use of small angle X-ray scattering (SAXS) for modeling macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, is presented.
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TL;DR: The structure of an Escherichia coli contaminating protein, acriflavine resistance protein B (AcrB), is compared with previously deposited AcrB structures and strategies are proposed to avoid this contamination.
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Determination of the Topological Shape of Integral Membrane Protein Light-Harvesting Complex LH2 from Photosynthetic Bacteria in the Detergent Solution by Small-Angle X-Ray Scattering
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TL;DR: The topological shape of the integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria Rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle X-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion.
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References
AMoRe: an automated package for molecular replacement
TL;DR: In this paper, a new molecular-replacement package is presented, which is an improvement on conventional methods, based on more powerful algorithms and a new conception that enables automation and rapid solution.
5.2K
Interpretation of small-angle scattering functions of dilute solutions and gases. A representation of the structures related to a one-particle scattering function
TL;DR: In this paper, the scalar field functions in physical and reciprocal space are expressed as a series of spherical harmonics Ylm, and the Hankel transformations of the multipole components are reduced to an algebraic problem by the introduction of Laguerre polynomials.
202
New developments in direct shape determination from small-angle scattering. 1. Theory and model calculations
D.I. Svergun,H.B. Stuhrmann +1 more
TL;DR: In this paper, a shape estimation method based on multipole expansion is described. But the shape refinement at higher resolution is ambiguous; a variety of shapes can be generated which fit the given intensity curve neatly, a criterion is given to select the most plausible solution in higher resolution studies.
164
Crystallographic structures of bovine copper-zinc superoxide dismutase reveal asymmetry in two subunits: functionally important three and five coordinate copper sites captured in the same crystal.
TL;DR: The pBSOD structure provides direct crystallographic evidence for the superoxide dismutase mechanism involving the breakage of the imidazole bridge between Cu and Zn and indicates a potential functional asymmetry between the subunits of CuZnSODs.
122
X‐ray Scattering Studies of Metalloproteins in Solution: a Quantitative Approach for Studying Molecular Conformations, a Quantitative Approach for Studying Molecular Conformations.
TL;DR: In this article, a model-independent approach based on the multipole expansion method using spherical harmonics was applied to obtain structural information on a variety of metalloproteins studied by synchrotron X-ray solution scattering.
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