This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1nmo

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:51, 10 April 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1nmo.jpg|left|200px]]
 
-
{{Structure
+
==Structural genomics, protein ybgI, unknown function==
-
|PDB= 1nmo |SIZE=350|CAPTION= <scene name='initialview01'>1nmo</scene>, resolution 2.20&Aring;
+
<StructureSection load='1nmo' size='340' side='right'caption='[[1nmo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
+
<table><tr><td colspan='2'>[[1nmo]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NMO 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]] 2.2&#8491;</td></tr>
-
|GENE= YBGI OR B0710 OR Z0861 OR ECS0735 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Escherichia coli, and Escherichia coli O157:H7])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmo OCA], [https://pdbe.org/1nmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nmo RCSB], [https://www.ebi.ac.uk/pdbsum/1nmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmo ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmo OCA], [http://www.ebi.ac.uk/pdbsum/1nmo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nmo RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/GCH1L_ECOLI GCH1L_ECOLI] Provides significant protection from radiation damage and may be involved in the degradation of radiation-damaged nucleotides.<ref>PMID:25049088</ref>
-
 
+
== Evolutionary Conservation ==
-
'''Structural genomics, protein ybgI, unknown function'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nm/1nmo_consurf.spt"</scriptWhenChecked>
-
BACKGROUND: The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function. RESULTS: The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid. CONCLUSION: The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1NMO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_and_escherichia_coli_o157:h7 Escherichia coli, and escherichia coli o157:h7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMO OCA].
+
</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=1nmo ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
== References ==
-
Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site., Ladner JE, Obmolova G, Teplyakov A, Howard AJ, Khil PP, Camerini-Otero RD, Gilliland GL, BMC Struct Biol. 2003 Sep 30;3:7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14519207 14519207]
+
<references/>
-
[[Category: Escherichia coli, and escherichia coli o157:h7]]
+
__TOC__
-
[[Category: Single protein]]
+
</StructureSection>
-
[[Category: Camerini-Otero, R D.]]
+
[[Category: Escherichia coli]]
-
[[Category: Gilliland, G L.]]
+
[[Category: Escherichia coli O157:H7]]
-
[[Category: Khil, P P.]]
+
[[Category: Large Structures]]
-
[[Category: Ladner, J E.]]
+
[[Category: Camerini-Otero RD]]
-
[[Category: Obmolova, G.]]
+
[[Category: Gilliland GL]]
-
[[Category: S2F, Structure 2.Function Project.]]
+
[[Category: Khil PP]]
-
[[Category: Teplyakov, A.]]
+
[[Category: Ladner JE]]
-
[[Category: hypothetical protein]]
+
[[Category: Obmolova G]]
-
[[Category: s2f]]
+
[[Category: Teplyakov A]]
-
[[Category: structural genomic]]
+
-
[[Category: structure 2 function project]]
+
-
[[Category: toroidal structure]]
+
-
[[Category: ybgi]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:32:30 2008''
+

Current revision

Structural genomics, protein ybgI, unknown function

PDB ID 1nmo

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/1nmo"
Personal tools