2knr: Difference between revisions

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[[Image:2knr.png|left|200px]]
==Solution structure of protein Atu0922 from A. tumefaciens. Northeast Structural Genomics Consortium target AtT13. Ontario Center for Structural Proteomics target ATC0905==
<StructureSection load='2knr' size='340' side='right' caption='[[2knr]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
== Structural highlights ==
[[2knr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens_str._c58 Agrobacterium tumefaciens str. c58]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KNR OCA]. <br>
<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kn/2knr_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
== Publication Abstract from PubMed ==
The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.


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A novel strategy for NMR resonance assignment and protein structure determination.,Lemak A, Gutmanas A, Chitayat S, Karra M, Fares C, Sunnerhagen M, Arrowsmith CH J Biomol NMR. 2011 Jan;49(1):27-38. Epub 2010 Dec 14. PMID:21161328<ref>PMID:21161328</ref>
The line below this paragraph, containing "STRUCTURE_2knr", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_2knr|  PDB=2knr  |  SCENE=  }}


===Solution structure of protein Atu0922 from A. tumefaciens. Northeast Structural Genomics Consortium target AtT13. Ontario Center for Structural Proteomics target ATC0905===
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
 
== References ==
 
<references/>
<!--
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The line below this paragraph, {{ABSTRACT_PUBMED_21161328}}, adds the Publication Abstract to the page
</StructureSection>
(as it appears on PubMed at http://www.pubmed.gov), where 21161328 is the PubMed ID number.
-->
{{ABSTRACT_PUBMED_21161328}}
 
==About this Structure==
[[2knr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens_str._c58 Agrobacterium tumefaciens str. c58]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KNR OCA].
 
==Reference==
<ref group="xtra">PMID:021161328</ref><references group="xtra"/>
[[Category: Agrobacterium tumefaciens str. c58]]
[[Category: Agrobacterium tumefaciens str. c58]]
[[Category: Arrowsmith, C H.]]
[[Category: Arrowsmith, C H.]]

Revision as of 11:28, 30 April 2014

Solution structure of protein Atu0922 from A. tumefaciens. Northeast Structural Genomics Consortium target AtT13. Ontario Center for Structural Proteomics target ATC0905Solution structure of protein Atu0922 from A. tumefaciens. Northeast Structural Genomics Consortium target AtT13. Ontario Center for Structural Proteomics target ATC0905

Structural highlights

2knr is a 1 chain structure with sequence from Agrobacterium tumefaciens str. c58. Full experimental information is available from OCA.

Activity: Glucokinase, with EC number 2.7.1.2

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

A novel strategy for NMR resonance assignment and protein structure determination.,Lemak A, Gutmanas A, Chitayat S, Karra M, Fares C, Sunnerhagen M, Arrowsmith CH J Biomol NMR. 2011 Jan;49(1):27-38. Epub 2010 Dec 14. PMID:21161328[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Lemak A, Gutmanas A, Chitayat S, Karra M, Fares C, Sunnerhagen M, Arrowsmith CH. A novel strategy for NMR resonance assignment and protein structure determination. J Biomol NMR. 2011 Jan;49(1):27-38. Epub 2010 Dec 14. PMID:21161328 doi:10.1007/s10858-010-9458-0
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