2qpd

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[[Image:2qpd.jpg|left|200px]]
 
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{{Structure
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==An unexpected outcome of surface-engineering an integral membrane protein: Improved crystallization of cytochrome ba3 oxidase from Thermus thermophilus==
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|PDB= 2qpd |SIZE=350|CAPTION= <scene name='initialview01'>2qpd</scene>, resolution 3.25&Aring;
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<StructureSection load='2qpd' size='340' side='right'caption='[[2qpd]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>
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<table><tr><td colspan='2'>[[2qpd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QPD FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span>
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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]] 3.25&#8491;</td></tr>
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|GENE= cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
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|DOMAIN=
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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=2qpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qpd OCA], [https://pdbe.org/2qpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qpd RCSB], [https://www.ebi.ac.uk/pdbsum/2qpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qpd ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1xme|1XME]], [[2qpe|2QPE]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qpd OCA], [http://www.ebi.ac.uk/pdbsum/2qpd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qpd RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8]
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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/qp/2qpd_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=2qpd ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Past work has shown that it is feasible to mutate surface residues of soluble proteins and to a lesser extent membrane proteins in order to improve their crystallization behavior. Described here is a successful application of this approach to the integral membrane protein Thermus thermophilus cytochrome ba(3) oxidase. Two mutant forms of this enzyme (I-K258R and I-K258R/II-E4Q) were created in which symmetrical crystal contacts within crystals of wild-type enzyme were modified. These mutant proteins had greatly shortened crystallization times, decreasing from approximately 30 d for the wild type to 1-3 d for the mutants, and crystallization was highly reproducible. Native-like proteins crystallize in space group P4(3)2(1)2, whereas the mutant proteins crystallize in space group P4(1)2(1)2 with a different packing arrangement. Crystals of the P4(3)2(1)2 form occasionally diffracted to 2.4-2.3 A resolution following controlled dehydration, while those of the P4(1)2(1)2 form routinely diffracted to between 3.0 and 2.6 A for crystals that had been cryoprotected but not dehydrated.
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'''An unexpected outcome of surface-engineering an integral membrane protein: Improved crystallization of cytochrome ba3 oxidase from Thermus thermophilus'''
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An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus.,Liu B, Luna VM, Chen Y, Stout CD, Fee JA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Dec 1;63(Pt, 12):1029-34. Epub 2007 Nov 21. PMID:18084085<ref>PMID:18084085</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2qpd" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Cytochrome ba(3) oxidase is an integral membrane protein identified in the thermophilic bacterium Thermus thermophilus. The enzyme has now been expressed recombinantly and purified with a histidine tag. As such, it crystallizes under similar conditions and in the same space group (P4(3)2(1)2) as the native protein. A novel cryoprotection scheme is described here to obtain high-resolution diffraction from these crystals, which involves soaking in a mixture of glycerol and ethylene glycol under a layer of oil. The unit-cell parameters for these crystals are larger than the native protein, apparently deriving from increased ordering of the N-terminus and an internal loop (residues 495-500) in subunit I. Hence, compared with native cytochrome ba(3) oxidase, the recombinant His-tagged protein is accommodated in an expanded but equally well ordered lattice via an alternate set of specific intermolecular contacts. The structure was refined against data to 2.3 angstroms resolution to an R factor of 21.7% and an R(free) of 23.7%.
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*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2QPD is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QPD OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus., Hunsicker-Wang LM, Pacoma RL, Chen Y, Fee JA, Stout CD, Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):340-3. Epub 2005, Feb 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15735345 15735345]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Cytochrome-c oxidase]]
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[[Category: Chen Y]]
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[[Category: Protein complex]]
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[[Category: Fee JA]]
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[[Category: Thermus thermophilus]]
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[[Category: Liu B]]
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[[Category: Chen, Y.]]
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[[Category: Luna VM]]
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[[Category: Fee, J A.]]
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[[Category: Stout CD]]
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[[Category: Liu, B.]]
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[[Category: Luna, V M.]]
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[[Category: Stout, C D.]]
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[[Category: copper]]
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[[Category: cytochrome ba3 oxidase]]
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[[Category: electron transport]]
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[[Category: formylation]]
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[[Category: heme,integral membrane protein]]
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[[Category: hydrogen ion transport]]
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[[Category: ion transport]]
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[[Category: iron]]
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[[Category: metal-binding]]
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[[Category: oxidoreductase]]
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[[Category: respiratory chain]]
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[[Category: transmembrane]]
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[[Category: transport]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:51:45 2008''
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Current revision

An unexpected outcome of surface-engineering an integral membrane protein: Improved crystallization of cytochrome ba3 oxidase from Thermus thermophilus

PDB ID 2qpd

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