2k54: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Solution NMR structure of protein Atu0742 from Agrobacterium Tumefaciens. Northeast Structural Genomics Consortium (NESG0) target AtT8. Ontario Center for Structural Proteomics target ATC0727 .==
==Solution NMR structure of protein Atu0742 from Agrobacterium Tumefaciens. Northeast Structural Genomics Consortium (NESG0) target AtT8. Ontario Center for Structural Proteomics target ATC0727 .==
<StructureSection load='2k54' size='340' side='right' caption='[[2k54]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
<StructureSection load='2k54' size='340' side='right'caption='[[2k54]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2k54]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrt5 Agrt5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K54 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K54 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2k54]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K54 FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGR_C_1343, Atu0742 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRT5])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2k54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k54 OCA], [http://pdbe.org/2k54 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k54 RCSB], [http://www.ebi.ac.uk/pdbsum/2k54 PDBsum], [http://www.topsan.org/Proteins/NESGC/2k54 TOPSAN]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2k54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k54 OCA], [https://pdbe.org/2k54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k54 RCSB], [https://www.ebi.ac.uk/pdbsum/2k54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k54 ProSAT], [https://www.topsan.org/Proteins/NESGC/2k54 TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A9CJY7_AGRFC A9CJY7_AGRFC]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/2k54_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/2k54_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 16: Line 19:
</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/main_output.php?pdb_ID=2k54 ConSurf].
</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/main_output.php?pdb_ID=2k54 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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<ref>PMID:21161328</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2k54" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Agrt5]]
[[Category: Agrobacterium fabrum str. C58]]
[[Category: Arrowsmith, C]]
[[Category: Large Structures]]
[[Category: Fares, C]]
[[Category: Arrowsmith C]]
[[Category: Gutmanas, A]]
[[Category: Fares C]]
[[Category: Lemak, A]]
[[Category: Gutmanas A]]
[[Category: Montelione, G T]]
[[Category: Lemak A]]
[[Category: Structural genomic]]
[[Category: Montelione GT]]
[[Category: Semesi, A]]
[[Category: Semesi A]]
[[Category: Yee, A]]
[[Category: Yee A]]
[[Category: Nesg]]
[[Category: Protein of unknown function]]
[[Category: PSI, Protein structure initiative]]
[[Category: Unknown function]]

Latest revision as of 09:44, 1 May 2024

Solution NMR structure of protein Atu0742 from Agrobacterium Tumefaciens. Northeast Structural Genomics Consortium (NESG0) target AtT8. Ontario Center for Structural Proteomics target ATC0727 .Solution NMR structure of protein Atu0742 from Agrobacterium Tumefaciens. Northeast Structural Genomics Consortium (NESG0) target AtT8. Ontario Center for Structural Proteomics target ATC0727 .

Structural highlights

2k54 is a 1 chain structure with sequence from Agrobacterium fabrum str. C58. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

A9CJY7_AGRFC

Evolutionary Conservation

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

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2k54&oldid=4135720"