Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1302-5. Epub 2005 Aug 16.

Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions.

Sugahara M, Asada Y, Ayama H, Ukawa H, Taka H, Kunishima N.

Source

Advanced Protein Crystallography Research Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.

Abstract

Heavy-atom Database System (HATODAS) is a WWW-based tool designed to assist the heavy-atom derivatization of proteins. The conventional procedure for the preparation of derivatives is usually a time-consuming 'trial-and-error' process. The present program provides a solution for this problem using a database of known heavy-atom derivatives. A database search suggests potential heavy-atom reagents for any target protein based on its amino-acid sequence and crystallization conditions. A mining of the database identified 93 preferred motifs for heavy-atom binding. The motifs are observed frequently at the actual heavy-atom-binding sites encountered in the process of structure determination.

PMID:: 16131765; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Supplemental Content

Related citations

Novel versatile cryoprotectants for heavy-atom derivatization of protein crystals. [Acta Crystallogr D Biol Crystallogr. 2006]
Novel versatile cryoprotectants for heavy-atom derivatization of protein crystals.
Sugahara M, Kunishima N. Acta Crystallogr D Biol Crystallogr. 2006 May; 62(Pt 5):520-6. Epub 2006 Apr 19.
HAD, a data bank of heavy-atom binding sites in protein crystals: a resource for use in multiple isomorphous replacement and anomalous scattering. [Acta Crystallogr D Biol Crystallogr. 1998]
HAD, a data bank of heavy-atom binding sites in protein crystals: a resource for use in multiple isomorphous replacement and anomalous scattering.
Islam SA, Carvin D, Sternberg MJ, Blundell TL. Acta Crystallogr D Biol Crystallogr. 1998 Nov 1; 54(Pt 6 Pt 1):1199-206.
Membrane's Eleven: heavy-atom derivatives of membrane-protein crystals. [Acta Crystallogr D Biol Crystallogr. 2006]
Membrane's Eleven: heavy-atom derivatives of membrane-protein crystals.
Morth JP, Sørensen TL, Nissen P. Acta Crystallogr D Biol Crystallogr. 2006 Aug; 62(Pt 8):877-82. Epub 2006 Jul 18.
Review Identification of motifs in protein sequences. [Curr Protoc Cell Biol. 2001]
Review Identification of motifs in protein sequences.
Sonnhammer EL, Wolfsberg TG. Curr Protoc Cell Biol. 2001 May; Appendix 1:Appendix 1C.
Review Protein identification by tandem mass spectrometry and sequence database searching. [Methods Mol Biol. 2007]
Review Protein identification by tandem mass spectrometry and sequence database searching.
Nesvizhskii AI. Methods Mol Biol. 2007; 367:87-119.

See reviews... See all...

Cited by 2 PubMed Central articles

The magic triangle goes MAD: experimental phasing with a bromine derivative. [Acta Crystallogr D Biol Crystallogr. 2010]
The magic triangle goes MAD: experimental phasing with a bromine derivative.
Beck T, Gruene T, Sheldrick GM. Acta Crystallogr D Biol Crystallogr. 2010 Apr; 66(Pt 4):374-80. Epub 2010 Mar 24.
Towards a rational approach for heavy-atom derivative screening in protein crystallography. [Acta Crystallogr D Biol Crystallogr. 2008]
Towards a rational approach for heavy-atom derivative screening in protein crystallography.
Agniswamy J, Joyce MG, Hammer CH, Sun PD. Acta Crystallogr D Biol Crystallogr. 2008 Apr; 64(Pt 4):354-67. Epub 2008 Mar 19.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives...
Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions.
Acta Crystallogr D Biol Crystallogr. 2005 Sep ;61(Pt 9):1302-5. Epub 2005 Aug 16 .

PubMed
The role of eicosanoids in the brain.
The role of eicosanoids in the brain.
Asia Pac J Clin Nutr. 2008 ;17 Suppl 1:220-8.

PubMed
Prevalence and correlates of depression, anxiety, and suicidality among universi...
Prevalence and correlates of depression, anxiety, and suicidality among university students.
Am J Orthopsychiatry. 2007 Oct ;77(4):534-42.

PubMed
Cyclophilin A as negative regulator of apoptosis by sequestering cytochrome c.
Cyclophilin A as negative regulator of apoptosis by sequestering cytochrome c.
Biochem Biophys Res Commun. 2010 Mar 5 ;393(2):325-30. Epub 2010 Feb 6 .

PubMed
The emerging role of ACE2 in physiology and disease.
The emerging role of ACE2 in physiology and disease.
J Pathol. 2007 May ;212(1):1-11.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: