2fdn: 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: @@
 ==2[4FE-4S] FERREDOXIN FROM CLOSTRIDIUM ACIDI-URICI==
-<StructureSection load='2fdn' size='340' side='right' caption='[[2fdn]], [[Resolution|resolution]] 0.94&Aring;' scene=''>
+<StructureSection load='2fdn' size='340' side='right'caption='[[2fdn]], [[Resolution|resolution]] 0.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2fdn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_acidurici Clostridium acidurici]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FDN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2fdn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gottschalkia_acidurici Gottschalkia acidurici]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FDN FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.94&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fdn RCSB], [http://www.ebi.ac.uk/pdbsum/2fdn PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<table>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdn OCA], [https://pdbe.org/2fdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fdn RCSB], [https://www.ebi.ac.uk/pdbsum/2fdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fdn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FER_GOTA9 FER_GOTA9] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.[UniProtKB:P50727]
 == 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/fd/2fdn_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/2fdn_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2fdn ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici has been solved using X-ray diffraction data extending to atomic resolution, 0.94 A, recorded at 100 K. The model was refined with anisotropic representation of atomic displacement parameters for all non-hydrogen atoms and with hydrogens riding on their parent atoms. Stereochemical restraints were applied to the protein chain but not to the iron-sulfur clusters. The final R factor is 10.03 % for all data. Inversion of the final least-squares matrix allowed direct estimation of the errors of individual parameters. The estimated errors in positions for protein main chain atoms are below 0.02 A and about 0.003 A for the heavier [4Fe-4S] cluster atoms. Significant differences between the stereochemistry of the two clusters and distortion of both of them from ideal Td tetrahedral symmetry can be defined in detail at this level of accuracy. Regions of alternative conformations include not only protein side chains but also two regions of the main chain. One such region is the loop of residues 25-29, which was highly disordered in the room temperature structure.
-Atomic resolution (0.94 A) structure of Clostridium acidurici ferredoxin. Detailed geometry of [4Fe-4S] clusters in a protein.,Dauter Z, Wilson KS, Sieker LC, Meyer J, Moulis JM Biochemistry. 1997 Dec 23;36(51):16065-73. PMID:9405040<ref>PMID:9405040</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Ferredoxin|Ferredoxin]]
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Clostridium acidurici]]
+[[Category: Gottschalkia acidurici]]
-[[Category: Dauter, Z.]]
+[[Category: Large Structures]]
-[[Category: Meyer, J.]]
+[[Category: Dauter Z]]
-[[Category: Moulis, J M.]]
+[[Category: Meyer J]]
-[[Category: Sieker, L C.]]
+[[Category: Moulis JM]]
-[[Category: Wilson, K S.]]
+[[Category: Sieker LC]]
-[[Category: Electron transport]]
+[[Category: Wilson KS]]
-[[Category: Iron-sulfur]]