3c0v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_3c0v", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...)
Current revision (14:04, 13 March 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3c0v.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of cytokinin-specific binding protein in complex with cytokinin and Ta6Br12==
-
The line below this paragraph, containing "STRUCTURE_3c0v", creates the "Structure Box" on the page.
+
<StructureSection load='3c0v' size='340' side='right'caption='[[3c0v]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3c0v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vigna_radiata Vigna radiata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C0V FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</scene>, <scene name='pdbligand=ZEA:(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL'>ZEA</scene></td></tr>
-
{{STRUCTURE_3c0v| PDB=3c0v | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c0v OCA], [https://pdbe.org/3c0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c0v RCSB], [https://www.ebi.ac.uk/pdbsum/3c0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c0v ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystal structure of cytokinin-specific binding protein in complex with cytokinin and Ta6Br12'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/PHBP_VIGRR PHBP_VIGRR] Binds the cytokinin trans-zeatin in vitro (PubMed:16998071, PubMed:18453695). Binds gibberellin A3 (GA3) in vitro (PubMed:25004979).<ref>PMID:16998071</ref> <ref>PMID:18453695</ref> <ref>PMID:25004979</ref>
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
The crystal structure of cytokinin-specific binding protein (CSBP) containing four independent molecules with 4 x 155 = 620 residues in the asymmetric unit of the P6(4) unit cell has been solved by three-wavelength MAD using 1.8 A resolution data recorded from a crystal derivatized with the dodecabromohexatantalum cation (Ta(6)Br(12))(2+). The diffraction data contained a very strong anomalous signal (allowing successful phasing even using peak SAD data alone) despite the fact that the five (Ta(6)Br(12))(2+) clusters found in the asymmetric unit have low occupancy (about 0.3). The derivative structure has been successfully refined to R = 0.158, providing interesting details on the geometry of the (Ta(6)Br(12))(2+) cluster, its interactions with the protein and on the backsoaking of a cytokinin ligand that was originally part of a CSBP-cytokinin complex in the native crystals used for (Ta(6)Br(12))(2+) derivatization. A simulation analysis of the phasing power of the (Ta(6)Br(12))(2+) ions at artificially imposed resolution limits shows that it is not possible to resolve the individual Ta atoms if the d(min) limit of the data is higher than 2.9 A. Additionally, for successful Ta identification the (Ta(6)Br(12))(2+) complex should be specifically bound and ordered. Good binding at the protein surface is facilitated by the presence of acidic groups, indicating higher pH buffer conditions to be preferable. In addition, the water channels in the crystal should be sufficiently wide (at least 11 A) to allow free diffusion of the (Ta(6)Br(12))(2+) ions on soaking. A retrospective look at the initial molecular-replacement calculations provides interesting insights into how the peculiar packing mode and strong bias of the molecular-replacement-phased electron-density maps had hindered successful solution of the structure by this method.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/3c0v_consurf.spt"</scriptWhenChecked>
-
3C0V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Vigna_radiata Vigna radiata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C0V OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
MAD phasing using the (Ta(6)Br(12))(2+) cluster: a retrospective study., Pasternak O, Bujacz A, Biesiadka J, Bujacz G, Sikorski M, Jaskolski M, Acta Crystallogr D Biol Crystallogr. 2008 May;64(Pt 5):595-606. Epub 2008, Apr 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18453695 18453695]
+
</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=3c0v ConSurf].
-
[[Category: Single protein]]
+
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Vigna radiata]]
[[Category: Vigna radiata]]
-
[[Category: Biesiadka, J.]]
+
[[Category: Biesiadka J]]
-
[[Category: Bujacz, A.]]
+
[[Category: Bujacz A]]
-
[[Category: Bujacz, G.]]
+
[[Category: Bujacz G]]
-
[[Category: Jaskolski, M.]]
+
[[Category: Jaskolski M]]
-
[[Category: Pasternak, O.]]
+
[[Category: Pasternak O]]
-
[[Category: Sikorski, M.]]
+
[[Category: Sikorski M]]
-
[[Category: Cytokinin]]
+
-
[[Category: Mad]]
+
-
[[Category: Pathogenesis-related protein]]
+
-
[[Category: Plant defense]]
+
-
[[Category: Plant protein]]
+
-
[[Category: Ta6br12 complex]]
+
-
[[Category: Zeatin]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 22 21:53:28 2008''
+

Current revision

Crystal structure of cytokinin-specific binding protein in complex with cytokinin and Ta6Br12

PDB ID 3c0v

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3c0v"
Personal tools