2e6u: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2e6u.gif|left|200px]]


{{Structure
==Crystal structure of hypothetical protein PH1109 from Pyrococcus horikoshii==
|PDB= 2e6u |SIZE=350|CAPTION= <scene name='initialview01'>2e6u</scene>, resolution 1.80&Aring;
<StructureSection load='2e6u' size='340' side='right'caption='[[2e6u]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>
<table><tr><td colspan='2'>[[2e6u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2czz 2czz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E6U 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]] 1.8&#8491;</td></tr>
|GENE= PH1109 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</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=2e6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6u OCA], [https://pdbe.org/2e6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e6u RCSB], [https://www.ebi.ac.uk/pdbsum/2e6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e6u ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6u OCA], [http://www.ebi.ac.uk/pdbsum/2e6u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2e6u RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/O58836_PYRHO O58836_PYRHO]
 
== Evolutionary Conservation ==
'''Crystal structure of hypothetical protein PH1109 from Pyrococcus horikoshii'''
[[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/e6/2e6u_consurf.spt"</scriptWhenChecked>
A novel and easy crystal-mounting technique was developed for the sulfur SAD method using Cr Kalpha radiation (2.29 A). Using this technique, the cryo-buffer and cryoloop around the protein crystal can be removed before data collection in order to eliminate their X-ray absorption. The superiority and reproducibility of the data sets with this mounting technique were demonstrated using tetragonal hen egg-white lysozyme crystals. The structure of a novel protein, PH1109, from Pyrococcus horikoshii OT3 was solved using this technique. At the wavelength of Cr Kalpha radiation, the anomalous signal |DeltaF|/|F| of PH1109 is expected to be 1.72% as this protein of 144 residues includes four methionines and two cysteines. Sulfur SAD phasing was performed using SHELXD and SHELXE. In the case of the data set obtained using this novel crystal-mounting technique, 54.9% of all residues were built with side chains automatically by RESOLVE. On the other hand, only 16.0% were built with side chains for the data set collected using the standard cryoloop. These results indicated that this crystal-mounting technique was superior to the standard loop-mounting method for the measurement of small anomalous differences at longer wavelength and yielded better results in sulfur-substructure solution and initial phasing. The present study demonstrates that the sulfur SAD method with a chromium source becomes enhanced and more practical for macromolecular structure determination using the new crystal-mounting technique.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
2E6U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. This structure supersedes the now removed PDB entry 2CZZ. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6U 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=2e6u ConSurf].
 
<div style="clear:both"></div>
==Reference==
__TOC__
Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method., Kitago Y, Watanabe N, Tanaka I, Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1013-21. Epub 2005, Jul 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16041065 16041065]
</StructureSection>
[[Category: Pyrococcus horikoshii]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: Kitago, Y.]]
[[Category: Kitago Y]]
[[Category: Min, Y.]]
[[Category: Min Y]]
[[Category: Tanaka, I.]]
[[Category: Tanaka I]]
[[Category: Watanabe, N.]]
[[Category: Watanabe N]]
[[Category: coa binding]]
[[Category: rossmann-like]]
[[Category: structural genomics consortium for research on gene expression system]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:44:41 2008''

Latest revision as of 16:49, 13 March 2024

Crystal structure of hypothetical protein PH1109 from Pyrococcus horikoshiiCrystal structure of hypothetical protein PH1109 from Pyrococcus horikoshii

Structural highlights

2e6u is a 1 chain structure with sequence from Pyrococcus horikoshii OT3. This structure supersedes the now removed PDB entry 2czz. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O58836_PYRHO

Evolutionary Conservation

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

2e6u, resolution 1.80Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2e6u&oldid=4088785"