1dgr: Difference between revisions

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[[Image:1dgr.gif|left|200px]]


{{Structure
==Refined crystal structure of canavalin from jack bean==
|PDB= 1dgr |SIZE=350|CAPTION= <scene name='initialview01'>1dgr</scene>, resolution 2.6&Aring;
<StructureSection load='1dgr' size='340' side='right'caption='[[1dgr]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE ION'>PO4</scene>
<table><tr><td colspan='2'>[[1dgr]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DGR FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=1dgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dgr OCA], [https://pdbe.org/1dgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dgr RCSB], [https://www.ebi.ac.uk/pdbsum/1dgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dgr ProSAT]</span></td></tr>
 
</table>
'''Refined crystal structure of canavalin from jack bean'''
== Function ==
 
[https://www.uniprot.org/uniprot/CANA_CANEN CANA_CANEN] Seed storage protein.
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
The structure of canavalin, the vicilin-class storage protein from jack bean, was refined to 1.7 A resolution in a highly twinned rhombohedral crystal of space group R3 and unit-cell parameters a = b = c = 83.0 A, alpha = beta = gamma = 111.1 degrees. The resulting R and R(free) were 0.176 and 0.245, respectively. The orthorhombic crystal structure (space group C222(1), unit-cell parameters a = 136.5, b = 150.3, c = 133.4 A) was also refined with threefold non-crystallographic symmetry restraints. R and R(free) were 0.181 and 0.226, respectively, for 2.6 A resolution data. No significant difference in the protein structure was seen between these two crystal forms, nor between these two and the hexagonal and cubic crystal forms reported elsewhere [Ko et al. (1993), Acta Cryst. D49, 478-489; Ko et al. (1993), Plant Physiol. 101, 729-744]. A phosphate ion was identified in the lumen of the C-terminal beta-barrel. Lattice interactions showed that the trimeric molecule could be well accommodated in both 'top-up' and 'bottom-up' orientations in a rhombohedral unit cell of the R3 crystal and explained the presence of a high twin fraction. The large inter-trimer stacking interface of the C222(1) crystal may account for its relative stability. Atomic force microscopy (AFM) investigations of the growth of three crystal forms of canavalin indicate the rhombohedral form to be unique. Unlike the other two crystal forms, it contains at least an order of magnitude more screw dislocations and stacking faults than any other macromolecular crystal yet studied, and it alone grows principally by generation of steps from the screw dislocations. The unusually high occurrence of the screw dislocations and stacking faults is attributed to mechanical stress produced by the alternate molecular orientations in the rhombohedral crystals and their organization into discrete domains or blocks. At boundaries of alternate domains, lattice strain is relieved by the formation of the screw dislocations.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dg/1dgr_consurf.spt"</scriptWhenChecked>
1DGR is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DGR OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin., Ko TP, Kuznetsov YG, Malkin AJ, Day J, McPherson A, Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):829-39. Epub 2001, May 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11375502 11375502]
</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=1dgr ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Canavalia ensiformis]]
[[Category: Canavalia ensiformis]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Ko, T P.]]
[[Category: Ko T-P]]
[[Category: McPherson, A.]]
[[Category: McPherson A]]
[[Category: PO4]]
[[Category: duplicated domains beta barrel helical loop]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:38:22 2008''

Latest revision as of 09:53, 7 February 2024

Refined crystal structure of canavalin from jack beanRefined crystal structure of canavalin from jack bean

Structural highlights

1dgr is a 9 chain structure with sequence from Canavalia ensiformis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CANA_CANEN Seed storage protein.

Evolutionary Conservation

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

1dgr, resolution 2.60Å

Drag the structure with the mouse to rotate

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