1ryq: Difference between revisions

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[[Image:1ryq.png|left|200px]]
==Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001==
<StructureSection load='1ryq' size='340' side='right' caption='[[1ryq]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ryq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RYQ FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ryq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ryq RCSB], [http://www.ebi.ac.uk/pdbsum/1ryq PDBsum], [http://www.topsan.org/Proteins/SECSG/1ryq TOPSAN]</span></td></tr>
<table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ry/1ryq_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The determination of protein structures on a genomic scale requires both computing capacity and efficiency increases at many stages along the complex process. By combining bioinformatics workflow-management techniques, cluster-based computing and popular crystallographic structure-determination software packages, an efficient and powerful new tool for structural biology/genomics has been developed. Using the workflow manager and a simple web interface, the researcher can, in a few easy steps, set up hundreds of structure-determination jobs, each using a slightly different set of program input parameters, thus efficiently screening parameter space for the optimal input-parameter combination, i.e. a set of parameters that leads to a successful structure determination. Upon completion, results from the programs are harvested, analyzed, sorted based on success and presented to the user via the web interface. This approach has been applied with success in more than 30 cases. Examples of successful structure determinations based on single-wavelength scattering (SAS) are described and include cases where the 'rational' crystallographer-based selection of input parameters values had failed.


{{STRUCTURE_1ryq|  PDB=1ryq  |  SCENE=  }}
Parameter-space screening: a powerful tool for high-throughput crystal structure determination.,Liu ZJ, Lin D, Tempel W, Praissman JL, Rose JP, Wang BC Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):520-7. Epub 2005, Apr 20. PMID:15858261<ref>PMID:15858261</ref>


===Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_15858261}}
 
==About this Structure==
[[1ryq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYQ OCA].


==See Also==
==See Also==
*[[RNA polymerase|RNA polymerase]]
*[[RNA polymerase|RNA polymerase]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:015858261</ref><ref group="xtra">PMID:015930619</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Adams, M W.W.]]
[[Category: Adams, M W.W.]]

Revision as of 03:09, 29 September 2014

Putative DNA-directed RNA polymerase, subunit e from Pyrococcus Furiosus Pfu-263306-001Putative DNA-directed RNA polymerase, subunit e from Pyrococcus Furiosus Pfu-263306-001

Structural highlights

1ryq is a 1 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:FirstGlance, OCA, RCSB, PDBsum, TOPSAN

Evolutionary Conservation

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

Publication Abstract from PubMed

The determination of protein structures on a genomic scale requires both computing capacity and efficiency increases at many stages along the complex process. By combining bioinformatics workflow-management techniques, cluster-based computing and popular crystallographic structure-determination software packages, an efficient and powerful new tool for structural biology/genomics has been developed. Using the workflow manager and a simple web interface, the researcher can, in a few easy steps, set up hundreds of structure-determination jobs, each using a slightly different set of program input parameters, thus efficiently screening parameter space for the optimal input-parameter combination, i.e. a set of parameters that leads to a successful structure determination. Upon completion, results from the programs are harvested, analyzed, sorted based on success and presented to the user via the web interface. This approach has been applied with success in more than 30 cases. Examples of successful structure determinations based on single-wavelength scattering (SAS) are described and include cases where the 'rational' crystallographer-based selection of input parameters values had failed.

Parameter-space screening: a powerful tool for high-throughput crystal structure determination.,Liu ZJ, Lin D, Tempel W, Praissman JL, Rose JP, Wang BC Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):520-7. Epub 2005, Apr 20. PMID:15858261[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Liu ZJ, Lin D, Tempel W, Praissman JL, Rose JP, Wang BC. Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):520-7. Epub 2005, Apr 20. PMID:15858261 doi:10.1107/S0907444905003239

1ryq, resolution 1.38Å

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