1d3w: Difference between revisions

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-[[Image:1d3w.gif|left|200px]]
-<!--
+==Crystal structure of ferredoxin 1 d15e mutant from azotobacter vinelandii at 1.7 angstrom resolution.==
-The line below this paragraph, containing "STRUCTURE_1d3w", creates the "Structure Box" on the page.
+<StructureSection load='1d3w' size='340' side='right'caption='[[1d3w]], [[Resolution|resolution]] 1.70&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'>[[1d3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3W 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-{{STRUCTURE_1d3w|  PDB=1d3w  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3w OCA], [https://pdbe.org/1d3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3w RCSB], [https://www.ebi.ac.uk/pdbsum/1d3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3w ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FER1_AZOVI FER1_AZOVI] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. This ferredoxin could play a role in regulating gene expression by interacting directly with DNA.
+== 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/d3/1d3w_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=1d3w ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of ferredoxin 1 d15e mutant from azotobacter vinelandii at 1.7 angstrom resolution.'''
+==See Also==
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The basis of the chemiosmotic theory is that energy from light or respiration is used to generate a trans-membrane proton gradient. This is largely achieved by membrane-spanning enzymes known as 'proton pumps. There is intense interest in experiments which reveal, at the molecular level, how protons are drawn through proteins. Here we report the mechanism, at atomic resolution, for a single long-range electron-coupled proton transfer. In Azotobacter vinelandii ferredoxin I, reduction of a buried iron-sulphur cluster draws in a solvent proton, whereas re-oxidation is 'gated' by proton release to the solvent. Studies of this 'proton-transferring module' by fast-scan protein film voltammetry, high-resolution crystallography, site-directed mutagenesis and molecular dynamics, reveal that proton transfer is exquisitely sensitive to the position and pK of a single amino acid. The proton is delivered through the protein matrix by rapid penetrative excursions of the side-chain carboxylate of a surface residue (Asp 15), whose pK shifts in response to the electrostatic charge on the iron-sulphur cluster. Our analysis defines the structural, dynamic and energetic requirements for proton courier groups in redox-driven proton-pumping enzymes.
-==About this Structure==
-D3W is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3W OCA].
-==Reference==
-Atomically defined mechanism for proton transfer to a buried redox centre in a protein., Chen K, Hirst J, Camba R, Bonagura CA, Stout CD, Burgess BK, Armstrong FA, Nature. 2000 Jun 15;405(6788):814-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10866206 10866206]
 [[Category: Azotobacter vinelandii]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Armstrong, F A.]]
+[[Category: Armstrong FA]]
-[[Category: Bonagura, C A.]]
+[[Category: Bonagura CA]]
-[[Category: Burges, B K.]]
+[[Category: Burges BK]]
-[[Category: Camba, R.]]
+[[Category: Camba R]]
-[[Category: Chen, K.]]
+[[Category: Chen K]]
-[[Category: Hirst, J.]]
+[[Category: Hirst J]]
-[[Category: Stout, C D.]]
+[[Category: Stout CD]]
-[[Category: Beta sheet]]
-[[Category: Electron transport]]
-[[Category: Ferredoxin]]
-[[Category: Iron-sulphur protein]]
-[[Category: Protein monomer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:25:24 2008''