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| | ==Fully automated NMR structure determination of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana== | | ==Fully automated NMR structure determination of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana== |
| - | <StructureSection load='2dcq' size='340' side='right' caption='[[2dcq]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2dcq' size='340' side='right'caption='[[2dcq]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dcq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dcq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DCQ FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vee|1vee]]</td></tr> | + | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vee|1vee]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RIKEN cDNA RAFL06-68-J04 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RIKEN cDNA RAFL06-68-J04 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2dcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dcq OCA], [http://pdbe.org/2dcq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dcq RCSB], [http://www.ebi.ac.uk/pdbsum/2dcq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dcq ProSAT]</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=2dcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dcq OCA], [https://pdbe.org/2dcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dcq RCSB], [https://www.ebi.ac.uk/pdbsum/2dcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dcq ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/STR4_ARATH STR4_ARATH]] Rhodanese domain-containing protein required for anchoring ferredoxin--NADP reductase to the thylakoid membranes and sustaining efficient linear electron flow (LEF).<ref>PMID:19682289</ref> | + | [[https://www.uniprot.org/uniprot/STR4_ARATH STR4_ARATH]] Rhodanese domain-containing protein required for anchoring ferredoxin--NADP reductase to the thylakoid membranes and sustaining efficient linear electron flow (LEF).<ref>PMID:19682289</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Arath]] | | [[Category: Arath]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Guntert, P]] | | [[Category: Guntert, P]] |
| | [[Category: Lopez-Mendez, B]] | | [[Category: Lopez-Mendez, B]] |
| Structural highlights
Function
[STR4_ARATH] Rhodanese domain-containing protein required for anchoring ferredoxin--NADP reductase to the thylakoid membranes and sustaining efficient linear electron flow (LEF).[1]
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
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.
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Juric S, Hazler-Pilepic K, Tomasic A, Lepedus H, Jelicic B, Puthiyaveetil S, Bionda T, Vojta L, Allen JF, Schleiff E, Fulgosi H. Tethering of ferredoxin:NADP+ oxidoreductase to thylakoid membranes is mediated by novel chloroplast protein TROL. Plant J. 2009 Dec;60(5):783-94. doi: 10.1111/j.1365-313X.2009.03999.x. Epub 2009 , Aug 13. PMID:19682289 doi:http://dx.doi.org/10.1111/j.1365-313X.2009.03999.x
- ↑ Lopez-Mendez B, Guntert P. Automated protein structure determination from NMR spectra. J Am Chem Soc. 2006 Oct 11;128(40):13112-22. PMID:17017791 doi:10.1021/ja061136l
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