1fnb: Difference between revisions

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-[[Image:1fnb.jpg|left|200px]]<br /><applet load="1fnb" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1fnb, resolution 1.7&Aring;" />
-'''REFINED CRYSTAL STRUCTURE OF SPINACH FERREDOXIN REDUCTASE AT 1.7 ANGSTROMS RESOLUTION: OXIDIZED, REDUCED, AND 2'-PHOSPHO-5'-AMP BOUND STATES'''<br />
-==Overview==
+==REFINED CRYSTAL STRUCTURE OF SPINACH FERREDOXIN REDUCTASE AT 1.7 ANGSTROMS RESOLUTION: OXIDIZED, REDUCED, AND 2'-PHOSPHO-5'-AMP BOUND STATES==
-The crystal structure of spinach ferredoxin-NADP(+)-oxidoreductase (FNR), determined by multiple isomorphous replacement at 2.6 A resolution, has been refined at 1.7 A resolution to an R-factor of 17.9%. The structure of FNR bound to the competitive inhibitor 2'-phospho-5'-AMP (P-AMP) has also been refined at 1.7 A to an R-factor of 17.4% and dithionite-reduced/P-AMP-bound FNR has been refined at 2.0 A to an R-factor of 14.9%. The P-AMP-bound structure was used to construct a model for the binding of NADP+. Over 200 solvation sites were included in each structure, and many of the best defined solvation sites stabilize buried turns. A bulk solvent correction obviated the need for a low-resolution data cutoff. An acidic side-chain likely to be responsible for the low pH requirement for crystallization has been identified. Three large networks of the hydrophobic side-chains help define the FNR structure. One of these contains a large cavity far from the active site, which coincides with the lone site of sequence heterogeneity in FNR, and may provide a site for membrane attachment. The reduced structure shows that Ser96 moves toward atom N-5 of FAD and a water molecule moves toward atom N-1 of FAD, while the flavin moiety remains planar. Possible sources of a proton that must be picked up upon reduction are discussed.
+<StructureSection load='1fnb' size='340' side='right'caption='[[1fnb]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1fnb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fnr 1fnr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FNB FirstGlance]. <br>
-FNB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=FAD:'>FAD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1FNR. Active as [http://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FNB OCA].
+</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fnb OCA], [https://pdbe.org/1fnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fnb RCSB], [https://www.ebi.ac.uk/pdbsum/1fnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fnb ProSAT]</span></td></tr>
-Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states., Bruns CM, Karplus PA, J Mol Biol. 1995 Mar 17;247(1):125-45. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7897656 7897656]
+</table>
-[[Category: Ferredoxin--NADP(+) reductase]]
+== Function ==
-[[Category: Single protein]]
+[https://www.uniprot.org/uniprot/FENR_SPIOL FENR_SPIOL] May play a key role in regulating the relative amounts of cyclic and non-cyclic electron flow to meet the demands of the plant for ATP and reducing power.
+== 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/fn/1fnb_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=1fnb ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Spinacia oleracea]]
-[[Category: Bruns, C M.]]
+[[Category: Bruns CM]]
-[[Category: Karplus, P A.]]
+[[Category: Karplus PA]]
-[[Category: FAD]]
-[[Category: PO4]]
-[[Category: SO4]]
-[[Category: ferredoxin(a))]]
-[[Category: oxidoreductase (nadp+(a)]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:40:30 2008''