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Quantum Chemistry Can Locally Improve Protein Crystal Structures

Ryde, Ulf LU and Nilsson, Kristina LU (2003) In Journal of the American Chemical Society 125(47). p.14232-14233
Abstract
We have re-refined the X-ray structure of the heme site in cytochrome c553, supplementing the crystallographic data with quantum chemical geometry optimizations, instead of the molecular mechanics force field used in standard crystallographic refinement. By comparing the resulting structure, obtained using medium-resolution data (170 pm), with an atomic-resolution structure (95 pm) of the same protein, we show that the inclusion of quantum chemical information into the refinement procedure improves the structure significantly. Thus, errors in the Fe-ligand distances are reduced from 3 to 32 pm in the low-resolution structure to 0-5 pm in the re-refined structure, one side-chain atom changes its conformation (a movement by 214 pm toward its... (More)
We have re-refined the X-ray structure of the heme site in cytochrome c553, supplementing the crystallographic data with quantum chemical geometry optimizations, instead of the molecular mechanics force field used in standard crystallographic refinement. By comparing the resulting structure, obtained using medium-resolution data (170 pm), with an atomic-resolution structure (95 pm) of the same protein, we show that the inclusion of quantum chemical information into the refinement procedure improves the structure significantly. Thus, errors in the Fe-ligand distances are reduced from 3 to 32 pm in the low-resolution structure to 0-5 pm in the re-refined structure, one side-chain atom changes its conformation (a movement by 214 pm toward its position in the high-resolution structure), and the R factors are improved by up to 0.018. Thus, quantum refinement may be a powerful method to obtain an accurate structure for interesting parts of a protein. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of the American Chemical Society
volume
125
issue
47
pages
14232 - 14233
publisher
The American Chemical Society
external identifiers
  • wos:000186722200011
  • scopus:0344012221
ISSN
1520-5126
DOI
10.1021/ja0365328
language
English
LU publication?
yes
id
50cd5e8f-cd04-4dad-81e9-0184926a9ad5 (old id 128835)
date added to LUP
2007-07-17 13:48:09
date last changed
2018-09-09 04:22:49
@article{50cd5e8f-cd04-4dad-81e9-0184926a9ad5,
  abstract     = {We have re-refined the X-ray structure of the heme site in cytochrome c553, supplementing the crystallographic data with quantum chemical geometry optimizations, instead of the molecular mechanics force field used in standard crystallographic refinement. By comparing the resulting structure, obtained using medium-resolution data (170 pm), with an atomic-resolution structure (95 pm) of the same protein, we show that the inclusion of quantum chemical information into the refinement procedure improves the structure significantly. Thus, errors in the Fe-ligand distances are reduced from 3 to 32 pm in the low-resolution structure to 0-5 pm in the re-refined structure, one side-chain atom changes its conformation (a movement by 214 pm toward its position in the high-resolution structure), and the R factors are improved by up to 0.018. Thus, quantum refinement may be a powerful method to obtain an accurate structure for interesting parts of a protein.},
  author       = {Ryde, Ulf and Nilsson, Kristina},
  issn         = {1520-5126},
  language     = {eng},
  number       = {47},
  pages        = {14232--14233},
  publisher    = {The American Chemical Society},
  series       = {Journal of the American Chemical Society},
  title        = {Quantum Chemistry Can Locally Improve Protein Crystal Structures},
  url          = {http://dx.doi.org/10.1021/ja0365328},
  volume       = {125},
  year         = {2003},
}