3ef4: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3ef4.png|left|200px]]
-<!--
+==Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans==
-The line below this paragraph, containing "STRUCTURE_3ef4", creates the "Structure Box" on the page.
+<StructureSection load='3ef4' size='340' side='right'caption='[[3ef4]], [[Resolution|resolution]] 1.18&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'>[[3ef4]] is a 3 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3EF4 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]] 1.18&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_3ef4|  PDB=3ef4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ef4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ef4 OCA], [https://pdbe.org/3ef4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ef4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ef4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ef4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A7VL37_9HYPH A7VL37_9HYPH]
+== 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/ef/3ef4_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=3ef4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The 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.
-===Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans===
+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<ref>PMID:19153470</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ef4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19153470}}, adds the Publication Abstract to the page
+*[[Pseudoazurin|Pseudoazurin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19153470 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19153470}}
+__TOC__
+</StructureSection>
-==About this Structure==
-EF4 is a 3 chains structure of sequences 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].
-==Reference==
-<ref group="xtra">PMID:19153470</ref><references group="xtra"/>
 [[Category: Hyphomicrobium denitrificans]]
-[[Category: Hira, D.]]
+[[Category: Large Structures]]
-[[Category: Nojiri, M.]]
+[[Category: Hira D]]
-[[Category: Suzuki, S.]]
+[[Category: Nojiri M]]
-[[Category: Blue copper protein]]
+[[Category: Suzuki S]]
-[[Category: Copper]]
-[[Category: Electron transfer]]
-[[Category: Electron transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  8 20:07:16 2009''