1cxr
From Proteopedia
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==AUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBIN(S22/I25) WITH SELF-CORRECTING DISTANCE GEOMETRY BASED NOAH/DIAMOD PROGRAMS== | ==AUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBIN(S22/I25) WITH SELF-CORRECTING DISTANCE GEOMETRY BASED NOAH/DIAMOD PROGRAMS== | ||
| - | <StructureSection load='1cxr' size='340' side='right'caption='[[1cxr | + | <StructureSection load='1cxr' size='340' side='right'caption='[[1cxr]]' scene=''> |
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1cxr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Crambe_hispanica_subsp._abyssinica Crambe hispanica subsp. abyssinica]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CXR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CXR FirstGlance]. <br> | <table><tr><td colspan='2'>[[1cxr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Crambe_hispanica_subsp._abyssinica Crambe hispanica subsp. abyssinica]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CXR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CXR FirstGlance]. <br> | ||
| - | </td></tr><tr id=' | + | </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'>[https://proteopedia.org/fgij/fg.htm?mol=1cxr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cxr OCA], [https://pdbe.org/1cxr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cxr RCSB], [https://www.ebi.ac.uk/pdbsum/1cxr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cxr 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=1cxr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cxr OCA], [https://pdbe.org/1cxr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cxr RCSB], [https://www.ebi.ac.uk/pdbsum/1cxr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cxr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/CRAM_CRAAB CRAM_CRAAB] The function of this hydrophobic plant seed protein is not known. | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=1cxr 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=1cxr ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The NOAH/DIAMOD program suite was used to automatically assign an experimental 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using feedback filtering and self-correcting distance geometry (SECODG). Automatically picked NOESY cross peaks were combined with 157 manually assigned peaks to start NOAH/DIAMOD calculations. At each cycle, DIAMOD was used to calculate an ensemble of 40 structures from these NOE distance constraints and random starting structures. The 10 structures with smallest target function values were analyzed by the structure-based filter, NOAH, and a new set of possible assignments was automatically generated based on chemical shifts and distance constraints violations. After 60 iterations and final energy minimization, the 10 structures with smallest target functions converged to 1.48 A for backbone atoms. Despite several missing chemical shifts, 426 of 613 NOE peaks were unambiguously assigned; 59 peaks were ambiguously assigned. The remaining 128 peaks picked automatically by FELIX are probably primarily noise peaks, with a few real peaks that were not assigned by NOAH due to the incomplete proton chemical shifts list. | ||
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| - | Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs.,Xu Y, Wu J, Gorenstein D, Braun W J Magn Reson. 1999 Jan;136(1):76-85. PMID:9887292<ref>PMID:9887292</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1cxr" style="background-color:#fffaf0;"></div> | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Crambe hispanica subsp. abyssinica]] | [[Category: Crambe hispanica subsp. abyssinica]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Braun | + | [[Category: Braun W]] |
| - | [[Category: Gorenstein | + | [[Category: Gorenstein D]] |
| - | [[Category: Wu | + | [[Category: Wu J]] |
| - | [[Category: Xu | + | [[Category: Xu Y]] |
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Revision as of 15:44, 13 March 2024
AUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBIN(S22/I25) WITH SELF-CORRECTING DISTANCE GEOMETRY BASED NOAH/DIAMOD PROGRAMS
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