Solution of the phase problem in the X-ray diffraction method for proteins with the nuclear magnetic resonance solution structure as initial model: Patterson search and refinement for the α-amylase inhibitor tendamistat

doi:10.1016/0022-2836(89)90574-3

Journal of Molecular Biology

Volume 206, Issue 4, 20 April 1989, Pages 669-676

https://doi.org/10.1016/0022-2836(89)90574-3 Get rights and content

Abstract

Patterson search calculations using the three-dimensional structure of the α-amylase inhibitor from Streptomyces tendae obtained from experimental nuclear magnetic resonance (n.m.r.) data were performed to study the possibility of solving the phase problem in the X-ray diffraction method with protein structures determined by n.m.r. Using all heavy atoms (C, N, O, S) of the residues 5 to 73 in the best n.m.r. structure of the α-amylase inhibitor (520 out of the 558 heavy atoms in the complete polypeptide chain), the maximum of the rotation function corresponded to the correct solution obtained by the previous independent determination of the crystal structure. However, additional local maxima, which are not significantly lower than the global maximum, also showed up. Performing the Patterson search with a model containing the backbone atoms and the heavy atoms of only the interior side-chains (399 atoms), which are much better defined by the n.m.r. data, the correct maximum was significantly higher than all other maxima. A translation search for the best orientation of the latter model yielded the correct solution. The energy-restrained crystallographic refinement was performed with this model to an R-factor of 26%. This corresponds approximately to the R-factor calculated for the X-ray crystal structure previously determined using the isomorphous replacement technique, if the residues 1 to 4 and 74 and all localized solvent molecules were removed from this structure. During the refinement the root-mean-square deviation between the two structures decreased from 1·03 Å to 0·26 Å for the polypeptide backbone and from 1·64 Å to 0·73 Å for all heavy atoms. There are no major local conformational differences between the two structures, with the single exception of the side-chain of Gln52.

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Citation Excerpt :
This encouraging result provided the basis for the complete NMR structure determination, which was available before Tendamistat could be crystallized [87,88]. Once the crystal structure was also available, it turned out that the two structures were identical in the global fold as well as in subtle local structural traits [89], and the X-ray structure of Tendamistat was eventually re-determined with a molecular replacement approach that used the NMR structure to solve the phase problem [90]. At this point, protein structure determination by NMR in solution got quite generally accepted, and we also learned through the grapevine that a new crystal structure determination of rat MT was started (see above and [85]).
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Journal of Molecular Biology

Solution of the phase problem in the X-ray diffraction method for proteins with the nuclear magnetic resonance solution structure as initial model: Patterson search and refinement for the α-amylase inhibitor tendamistat

Abstract

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J. Mol. Biol

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Methods Enzymol

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Science