1j5d: Difference between revisions

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-{{Seed}}
-[[Image:1j5d.png|left|200px]]
-<!--
+==SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803-MINIMIZED AVERAGE STRUCTURE==
-The line below this paragraph, containing "STRUCTURE_1j5d", creates the "Structure Box" on the page.
+<StructureSection load='1j5d' size='340' side='right'caption='[[1j5d]]' 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'>[[1j5d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803 Synechocystis sp. PCC 6803]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1i0y 1i0y]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J5D 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">Solution NMR</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></td></tr>
-{{STRUCTURE_1j5d|  PDB=1j5d  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5d OCA], [https://pdbe.org/1j5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j5d RCSB], [https://www.ebi.ac.uk/pdbsum/1j5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j5d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PLAS_SYNY3 PLAS_SYNY3] Participates in electron transfer between P700 and the cytochrome b6-f complex in photosystem I.[HAMAP-Rule:MF_00566]
+== 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/j5/1j5d_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=1j5d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The NMR solution structure of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803 is here reported. The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful NOESY cross-peaks, 18 1D NOEs, 26 T(1) values, 96 dihedral angle constraints, and 18 H-bonds. The detection of broad hyperfine-shifted signals and their full assignment allowed the identification of the copper(II) ligands and the determination of the Cu-S-C-H dihedral angle for the coordinated cysteine. The global root-mean-square deviation from the mean structure for the solution structure family is 0.72 +/- 0.14 and 1.16 +/- 0.17 A for backbone and heavy atoms, respectively. The structure is overall quite satisfactory and represents a breakthrough, in that it includes paramagnetic copper proteins among the metalloproteins for which solution structures can be afforded. The comparison with the available X-ray structure of a triple mutant is also performed.
-===SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803-MINIMIZED AVERAGE STRUCTURE===
+The first solution structure of a paramagnetic copper(II) protein: the case of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803.,Bertini I, Ciurli S, Dikiy A, Fernandez CO, Luchinat C, Safarov N, Shumilin S, Vila AJ J Am Chem Soc. 2001 Mar 14;123(10):2405-13. PMID:11456890<ref>PMID:11456890</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1j5d" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11456890}}, adds the Publication Abstract to the page
+*[[Plastocyanin 3D structures|Plastocyanin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11456890 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11456890}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-J5D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1i0y 1i0y]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5D OCA].
+[[Category: Synechocystis sp. PCC 6803]]
+[[Category: Bertini I]]
-==Reference==
+[[Category: Ciurli S]]
-The first solution structure of a paramagnetic copper(II) protein: the case of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803., Bertini I, Ciurli S, Dikiy A, Fernandez CO, Luchinat C, Safarov N, Shumilin S, Vila AJ, J Am Chem Soc. 2001 Mar 14;123(10):2405-13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11456890 11456890]
+[[Category: Dikiy A]]
-[[Category: Single protein]]
+[[Category: Fernandez CO]]
-[[Category: Synechocystis sp.]]
+[[Category: Luchinat C]]
-[[Category: Bertini, I.]]
+[[Category: Safarov N]]
-[[Category: Ciurli, S.]]
+[[Category: Shumilin S]]
-[[Category: Dikiy, A.]]
+[[Category: Vila AJ]]
-[[Category: Fernandez, C O.]]
-[[Category: Luchinat, C.]]
-[[Category: Safarov, N.]]
-[[Category: Shumilin, S.]]
-[[Category: Vila, A J.]]
-[[Category: Copper protein beta barrel electron transfer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 14:31:35 2008''