3kjr: Difference between revisions

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-{{Seed}}
-[[Image:3kjr.png|left|200px]]
-<!--
+==Crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis determined using SlipChip based microfluidics==
-The line below this paragraph, containing "STRUCTURE_3kjr", creates the "Structure Box" on the page.
+<StructureSection load='3kjr' size='340' side='right'caption='[[3kjr]], [[Resolution|resolution]] 1.95&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'>[[3kjr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Babesia_bovis_T2Bo Babesia bovis T2Bo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KJR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KJR 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]] 1.95&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr>
-{{STRUCTURE_3kjr|  PDB=3kjr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kjr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kjr OCA], [https://pdbe.org/3kjr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kjr RCSB], [https://www.ebi.ac.uk/pdbsum/3kjr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kjr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A7ASX7_BABBO A7ASX7_BABBO] Bifunctional enzyme. Involved in de novo dTMP biosynthesis. Key enzyme in folate metabolism (By similarity).[PIRNR:PIRNR000389]
+== 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/kj/3kjr_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/main_output.php?pdb_ID=3kjr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+This paper describes two SlipChip-based approaches to protein crystallization: a SlipChip-based free interface diffusion (FID) method and a SlipChip-based composite method that simultaneously performs microbatch and FID crystallization methods in a single device. The FID SlipChip was designed to screen multiple reagents, each at multiple diffusion equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis, against 48 different reagents at five different equilibration times each, consuming 12 microL of each protein for a total of 480 experiments using three SlipChips. The composite SlipChip was designed to screen multiple reagents, each at multiple mixing ratios and multiple equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis. To prevent cross-contamination while keeping the solution in the neck channels for FID stable, the plates of the SlipChip were etched with a pattern of nanowells. This nanopattern was used to increase the contact angle of aqueous solutions on the surface of the silanized glass. The composite SlipChip increased the number of successful crystallization conditions and identified more conditions for crystallization than separate FID and microbatch screenings. Crystallization experiments were scaled up in well plates using conditions identified during the SlipChip screenings, and X-ray diffraction data were obtained to yield the protein structure of dihydrofolate reductase/thymidylate synthase at 1.95 A resolution. This free-interface diffusion approach provides a convenient and high-throughput method of setting up gradients in microfluidic devices and may find additional applications in cell-based assays.
-===Crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis determined using SlipChip based microfluidics===
+Multiparameter screening on SlipChip used for nanoliter protein crystallization combining free interface diffusion and microbatch methods.,Li L, Du W, Ismagilov RF J Am Chem Soc. 2010 Jan 13;132(1):112-9. PMID:20000709<ref>PMID:20000709</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3kjr" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20000709}}, adds the Publication Abstract to the page
+*[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20000709 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20000709}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Babesia bovis T2Bo]]
-KJR is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Babesia_bovis_t2bo Babesia bovis t2bo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KJR OCA].
+[[Category: Large Structures]]
+[[Category: Du W]]
-==Reference==
+[[Category: Edwards TE]]
-<ref group="xtra">PMID:20000709</ref><references group="xtra"/>
+[[Category: Ismagilov RF]]
-[[Category: Babesia bovis t2bo]]
+[[Category: Li L]]
-[[Category: Thymidylate synthase]]
+[[Category: Phan I]]
-[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure.]]
+[[Category: Stacy R]]
-[[Category: Du, W.]]
+[[Category: Staker BL]]
-[[Category: Edwards, T E.]]
-[[Category: Ismagilov, R F.]]
-[[Category: Li, L.]]
-[[Category: Phan, I.]]
-[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
-[[Category: Stacy, R.]]
-[[Category: Staker, B L.]]
-[[Category: Accelerated technologies center for gene to 3d structure]]
-[[Category: Atcg3d]]
-[[Category: Methyltransferase]]
-[[Category: Microfluidic]]
-[[Category: Protein structure initiative]]
-[[Category: Psi-2]]
-[[Category: Seattle structural genomics center for infectious disease]]
-[[Category: Slipchip]]
-[[Category: Ssgcid]]
-[[Category: Structural genomic]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 28 10:57:59 2010''