3ef4: Difference between revisions
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==Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans== | ==Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans== | ||
<StructureSection load='3ef4' size='340' side='right' caption='[[3ef4]], [[Resolution|resolution]] 1.18Å' scene=''> | <StructureSection load='3ef4' size='340' side='right' caption='[[3ef4]], [[Resolution|resolution]] 1.18Å' scene=''> | ||
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<table><tr><td colspan='2'>[[3ef4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Hyphomicrobium_denitrificans Hyphomicrobium denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EF4 FirstGlance]. <br> | <table><tr><td colspan='2'>[[3ef4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Hyphomicrobium_denitrificans Hyphomicrobium denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EF4 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ef4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ef4 OCA], [http://pdbe.org/3ef4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ef4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ef4 PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ef4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ef4 OCA], [http://pdbe.org/3ef4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ef4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ef4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ef4 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ef/3ef4_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ef/3ef4_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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[[Category: Suzuki, S]] | [[Category: Suzuki, S]] | ||
[[Category: Blue copper protein]] | [[Category: Blue copper protein]] | ||
[[Category: Copper]] | |||
[[Category: Electron transfer]] | [[Category: Electron transfer]] | ||
[[Category: Electron transport]] | [[Category: Electron transport]] | ||
Revision as of 00:51, 3 December 2018
Crystal structure of native pseudoazurin from Hyphomicrobium denitrificansCrystal structure of native pseudoazurin from Hyphomicrobium denitrificans
Structural highlights
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 PubMedThe crystal structure of native pseudoazurin (HdPAz) from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans has been determined at a resolution of 1.18 A. After refinement with SHELX employing anisotropic displacement parameters and riding H atoms, R(work) and R(free) were 0.135 and 0.169, respectively. Visualization of the anisotropic displacement parameters as thermal ellipsoids provided insight into the atomic motion within the perturbed type 1 Cu site. The asymmetric unit includes three HdPAz molecules which are tightly packed by head-to-head cupredoxin dimer formation. The shape of the Cu-atom ellipsoid implies significant vibrational motion diagonal to the equatorial xy plane defined by the three ligands (two His and one Cys). The geometric parameters of the type 1 Cu site in the HdPAz structure differ unambiguously from those of other pseudoazurins. It is demonstrated that their structural aspects are consistent with the unique visible absorption spectrum. Atomic resolution structure of pseudoazurin from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans: structural insights into its spectroscopic properties.,Hira D, Nojiri M, Suzuki S Acta Crystallogr D Biol Crystallogr. 2009 Jan;65(Pt 1):85-92. Epub 2008, Dec 18. PMID:19153470[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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