Quantum Chemistry Can Locally Improve Protein Crystal Structures
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/128835
- author
- Ryde, Ulf LU and Nilsson, Kristina LU
- organization
- publishing date
- 2003
- 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 (ACS)
- external identifiers
-
- wos:000186722200011
- scopus:0344012221
- ISSN
- 1520-5126
- DOI
- 10.1021/ja0365328
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
- id
- 50cd5e8f-cd04-4dad-81e9-0184926a9ad5 (old id 128835)
- date added to LUP
- 2016-04-01 16:42:45
- date last changed
- 2023-01-24 02:30:52
@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 (ACS)}}, series = {{Journal of the American Chemical Society}}, title = {{Quantum Chemistry Can Locally Improve Protein Crystal Structures}}, url = {{https://lup.lub.lu.se/search/files/135490836/62_cytc.pdf}}, doi = {{10.1021/ja0365328}}, volume = {{125}}, year = {{2003}}, }