2dcq

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{{STRUCTURE_2dcq| PDB=2dcq | SCENE= }}
{{STRUCTURE_2dcq| PDB=2dcq | SCENE= }}
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'''Fully automated NMR structure determination of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana'''
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===Fully automated NMR structure determination of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana===
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==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 17017791 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17017791}}
==About this Structure==
==About this Structure==
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2DCQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCQ OCA].
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2DCQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCQ OCA].
==Reference==
==Reference==
Automated protein structure determination from NMR spectra., Lopez-Mendez B, Guntert P, J Am Chem Soc. 2006 Oct 11;128(40):13112-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17017791 17017791]
Automated protein structure determination from NMR spectra., Lopez-Mendez B, Guntert P, J Am Chem Soc. 2006 Oct 11;128(40):13112-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17017791 17017791]
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Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana., Pantoja-Uceda D, Lopez-Mendez B, Koshiba S, Inoue M, Kigawa T, Terada T, Shirouzu M, Tanaka A, Seki M, Shinozaki K, Yokoyama S, Guntert P, Protein Sci. 2005 Jan;14(1):224-30. Epub 2004 Dec 2. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15576557 15576557]
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NMR assignment of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana., Pantoja-Uceda D, Lopez-Mendez B, Koshiba S, Kigawa T, Shirouzu M, Terada T, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Hirota H, Yoshida M, Tanaka A, Osanai T, Seki M, Shinozaki K, Yokoyama S, Guntert P, J Biomol NMR. 2004 Jun;29(2):207-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15014235 15014235]
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: Fully automated structure determination]]
[[Category: Fully automated structure determination]]
[[Category: Rhodanese domain]]
[[Category: Rhodanese domain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:10:56 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:55:50 2008''

Revision as of 23:55, 28 July 2008

Image:2dcq.png

Template:STRUCTURE 2dcq

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

Template:ABSTRACT PUBMED 17017791

About this Structure

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

Reference

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

Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana., Pantoja-Uceda D, Lopez-Mendez B, Koshiba S, Inoue M, Kigawa T, Terada T, Shirouzu M, Tanaka A, Seki M, Shinozaki K, Yokoyama S, Guntert P, Protein Sci. 2005 Jan;14(1):224-30. Epub 2004 Dec 2. PMID:15576557

NMR assignment of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana., Pantoja-Uceda D, Lopez-Mendez B, Koshiba S, Kigawa T, Shirouzu M, Terada T, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Hirota H, Yoshida M, Tanaka A, Osanai T, Seki M, Shinozaki K, Yokoyama S, Guntert P, J Biomol NMR. 2004 Jun;29(2):207-8. PMID:15014235

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