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A large-scale, high-efficiency and low-cost platform for structural genomics studies

Su, Xiao Dong LU ; Liang, Yuhe; Li, Lanfen; Nan, Jie LU ; Bröstromer, Erik; Liu, Peng; Dong, Yuhui and Xian, Dingchang (2006) In Acta Crystallographica. Section D: Biological Crystallography 62(Pt 8). p.51-843
Abstract

A large-scale, high-efficiency and low-cost platform based on a Beckman Coulter Biomek FX and custom-made automation systems for structural genomics has been set up at Peking University, Beijing, People's Republic of China. This platform has the capacity to process up to 2000 genes per year for structural and functional analyses. Bacillus subtilis, a model organism for Gram-positive bacteria, and Streptococcus mutans, a major pathogen of dental caries, were selected as the main targets. To date, more than 470 B. subtilis and 1200 S. mutans proteins and hundreds of proteins from other sources, including human liver proteins, have been selected as targets for this platform. The selected genes are mainly related to important metabolism... (More)

A large-scale, high-efficiency and low-cost platform based on a Beckman Coulter Biomek FX and custom-made automation systems for structural genomics has been set up at Peking University, Beijing, People's Republic of China. This platform has the capacity to process up to 2000 genes per year for structural and functional analyses. Bacillus subtilis, a model organism for Gram-positive bacteria, and Streptococcus mutans, a major pathogen of dental caries, were selected as the main targets. To date, more than 470 B. subtilis and 1200 S. mutans proteins and hundreds of proteins from other sources, including human liver proteins, have been selected as targets for this platform. The selected genes are mainly related to important metabolism pathways and/or have potential relevance for drug design. To date, 40 independent structures have been determined; of these 11 are in the category of novel structures by the criterion of having less than 30% sequence identity to known structures. More than 13 structures were determined by SAD/MAD phasing. The macromolecular crystallography beamline at the Beijing Synchrotron Radiation Facility and modern phasing programs have been crucial components of the operation of the platform. The idea and practice of the genomic approach have been successfully adopted in a moderately funded structural biology program and it is believed this adaptation will greatly improve the production of protein structures. The goal is to be able to solve a protein structure of moderate difficulty at a cost about US 10,000 dollars.

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Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
keywords
Bacillus subtilis, Bacterial Proteins, Biomedical Research, Genome, Bacterial, Genomics, Protein Structure, Tertiary, Streptococcus mutans
in
Acta Crystallographica. Section D: Biological Crystallography
volume
62
issue
Pt 8
pages
9 pages
publisher
International Union of Crystallography
external identifiers
  • scopus:33746425844
ISSN
0907-4449
DOI
10.1107/S0907444906024395
language
English
LU publication?
yes
id
fbec3ad6-c504-45ce-be6e-ddc0b5ce7612
date added to LUP
2016-09-07 22:54:05
date last changed
2017-06-26 10:10:16
@article{fbec3ad6-c504-45ce-be6e-ddc0b5ce7612,
  abstract     = {<p>A large-scale, high-efficiency and low-cost platform based on a Beckman Coulter Biomek FX and custom-made automation systems for structural genomics has been set up at Peking University, Beijing, People's Republic of China. This platform has the capacity to process up to 2000 genes per year for structural and functional analyses. Bacillus subtilis, a model organism for Gram-positive bacteria, and Streptococcus mutans, a major pathogen of dental caries, were selected as the main targets. To date, more than 470 B. subtilis and 1200 S. mutans proteins and hundreds of proteins from other sources, including human liver proteins, have been selected as targets for this platform. The selected genes are mainly related to important metabolism pathways and/or have potential relevance for drug design. To date, 40 independent structures have been determined; of these 11 are in the category of novel structures by the criterion of having less than 30% sequence identity to known structures. More than 13 structures were determined by SAD/MAD phasing. The macromolecular crystallography beamline at the Beijing Synchrotron Radiation Facility and modern phasing programs have been crucial components of the operation of the platform. The idea and practice of the genomic approach have been successfully adopted in a moderately funded structural biology program and it is believed this adaptation will greatly improve the production of protein structures. The goal is to be able to solve a protein structure of moderate difficulty at a cost about US 10,000 dollars.</p>},
  author       = {Su, Xiao Dong and Liang, Yuhe and Li, Lanfen and Nan, Jie and Bröstromer, Erik and Liu, Peng and Dong, Yuhui and Xian, Dingchang},
  issn         = {0907-4449},
  keyword      = {Bacillus subtilis,Bacterial Proteins,Biomedical Research,Genome, Bacterial,Genomics,Protein Structure, Tertiary,Streptococcus mutans},
  language     = {eng},
  number       = {Pt 8},
  pages        = {51--843},
  publisher    = {International Union of Crystallography},
  series       = {Acta Crystallographica. Section D: Biological Crystallography},
  title        = {A large-scale, high-efficiency and low-cost platform for structural genomics studies},
  url          = {http://dx.doi.org/10.1107/S0907444906024395},
  volume       = {62},
  year         = {2006},
}