2dcq: Difference between revisions

Revision as of 00:10, 4 May 2008

Fully automated NMR structure determination of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana

OverviewOverview

Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus chemical shift assignments for all (1)H, (13)C, and (15)N nuclei, the assignment of NOESY cross-peaks, the generation of distance restraints, and the calculation of the three-dimensional structure by torsion angle dynamics. The resulting, preliminary structure serves as additional input to the second stage of the procedure, in which a new ensemble of chemical shift assignments and a refined structure are calculated. The three-dimensional structures of three 12-16 kDa proteins computed with the FLYA algorithm coincided closely with the conventionally determined structures. Deviations were below 0.95 A for the backbone atom positions, excluding the flexible chain termini. 96-97% of all backbone and side-chain chemical shifts in the structured regions were assigned to the correct residues. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination.

About this StructureAbout this Structure

2DCQ is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.

ReferenceReference

Automated protein structure determination from NMR spectra., Lopez-Mendez B, Guntert P, J Am Chem Soc. 2006 Oct 11;128(40):13112-22. PMID:17017791 Page seeded by OCA on Sun May 4 00:10:56 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 [[Image:2dcq.gif|left|200px]]
- {{Structure
+<!--
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+The line below this paragraph, containing "STRUCTURE_2dcq", creates the "Structure Box" on the page.
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+You may change the PDB parameter (which sets the PDB file loaded into the applet)
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+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-|GENE= RIKEN cDNA RAFL06-68-J04 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
+-->
-|DOMAIN=
+{{STRUCTURE_2dcq|  PDB=2dcq  |  SCENE=  }}
-|RELATEDENTRY=[[1vee|1VEE]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dcq OCA], [http://www.ebi.ac.uk/pdbsum/2dcq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dcq RCSB]</span>
-}}
 '''Fully automated NMR structure determination of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana'''
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 [[Category: Guntert, P.]]
 [[Category: Lopez-Mendez, B.]]
-[[Category: flya algorithm]]
+[[Category: Flya algorithm]]
-[[Category: fully automated structure determination]]
+[[Category: Fully automated structure determination]]
-[[Category: rhodanese domain]]
+[[Category: Rhodanese domain]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 00:10:56 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:32:56 2008''