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

Werner Braun, Otto Epp, Kurt Wüthrich, Robert Huber

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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.

Original languageEnglish
Pages (from-to)669-676
Number of pages8
JournalJournal of Molecular Biology
Volume206
Issue number4
DOIs
StatePublished - Apr 20 1989
Externally publishedYes

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Amylases
X-Ray Diffraction
R388
Magnetic Resonance Spectroscopy
Proteins
Peptides
Streptomyces
X-Rays
tendamistate

ASJC Scopus subject areas

  • Virology

Cite this

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title = "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 = "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 {\AA} to 0·26 {\AA} for the polypeptide backbone and from 1·64 {\AA} to 0·73 {\AA} 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.",
author = "Werner Braun and Otto Epp and Kurt W{\"u}thrich and Robert Huber",
year = "1989",
month = "4",
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language = "English",
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T1 - 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

AU - Braun, Werner

AU - Epp, Otto

AU - Wüthrich, Kurt

AU - Huber, Robert

PY - 1989/4/20

Y1 - 1989/4/20

N2 - 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.

AB - 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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