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1ryq

From Proteopedia

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[[Image:1ryq.jpg|left|200px]]<br /><applet load="1ryq" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ryq, resolution 1.38&Aring;" />
 
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'''Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001'''<br />
 
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==Overview==
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==Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001==
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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.
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<StructureSection load='1ryq' size='340' side='right'caption='[[1ryq]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ryq]] is a 1 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=1RYQ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.38&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ryq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryq OCA], [https://pdbe.org/1ryq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ryq RCSB], [https://www.ebi.ac.uk/pdbsum/1ryq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ryq ProSAT], [https://www.topsan.org/Proteins/SECSG/1ryq TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SPT4_PYRFU SPT4_PYRFU] Stimulates transcription elongation.<ref>PMID:21386817</ref> <ref>PMID:21187417</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ry/1ryq_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ryq ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1RYQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYQ OCA].
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
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==Reference==
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<references/>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15858261 15858261]
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
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[[Category: Single protein]]
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[[Category: Adams MWW]]
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[[Category: Adams, M W.W.]]
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[[Category: Arendall III WB]]
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[[Category: Brereton, P S.]]
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[[Category: Brereton PS]]
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[[Category: Chen, L.]]
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[[Category: Chen L]]
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[[Category: II, F L.Poole.]]
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[[Category: Izumi M]]
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[[Category: III, W B.Arendall.]]
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[[Category: Jenney Jr FE]]
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[[Category: Izumi, M.]]
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[[Category: Lee HS]]
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[[Category: Jr., F E.Jenney.]]
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[[Category: Liu Z-J]]
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[[Category: Lee, H S.]]
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[[Category: Poole II FL]]
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[[Category: Liu, Z J.]]
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[[Category: Richardson DC]]
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[[Category: Richardson, D C.]]
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[[Category: Richardson JS]]
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[[Category: Richardson, J S.]]
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[[Category: Rose JP]]
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[[Category: Rose, J P.]]
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[[Category: Shah A]]
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[[Category: SECSG, Southeast Collaboratory for Structural Genomics.]]
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[[Category: Shah C]]
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[[Category: Shah, A.]]
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[[Category: Sugar FJ]]
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[[Category: Shah, C.]]
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[[Category: Tempel W]]
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[[Category: Sugar, F J.]]
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[[Category: Wang B-C]]
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[[Category: Tempel, W.]]
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[[Category: Wang, B C.]]
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[[Category: ZN]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: rna polymerase]]
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[[Category: secsg]]
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[[Category: southeast collaboratory for structural genomics]]
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[[Category: structural genomics]]
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[[Category: zinc]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:56:03 2008''
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Current revision

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

PDB ID 1ryq

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