1j5c: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1j5c.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1j5c", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1j5c|  PDB=1j5c  |  SCENE=  }}
'''SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803'''


==SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803==
<StructureSection load='1j5c' size='340' side='right'caption='[[1j5c]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1j5c]] 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=1i0w 1i0w]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J5C FirstGlance]. <br>
</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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5c OCA], [https://pdbe.org/1j5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j5c RCSB], [https://www.ebi.ac.uk/pdbsum/1j5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j5c 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/j5/1j5c_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=1j5c 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.


==Overview==
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>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1J5C 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=1i0w 1i0w]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5C OCA].
</div>
<div class="pdbe-citations 1j5c" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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]
*[[Plastocyanin 3D structures|Plastocyanin 3D structures]]
[[Category: Single protein]]
== References ==
[[Category: Synechocystis sp.]]
<references/>
[[Category: Bertini, I.]]
__TOC__
[[Category: Ciurli, S.]]
</StructureSection>
[[Category: Dikiy, A.]]
[[Category: Large Structures]]
[[Category: Fernandez, C O.]]
[[Category: Synechocystis sp. PCC 6803]]
[[Category: Luchinat, C.]]
[[Category: Bertini I]]
[[Category: Safarov, N.]]
[[Category: Ciurli S]]
[[Category: Shumilin, S.]]
[[Category: Dikiy A]]
[[Category: Vila, A J.]]
[[Category: Fernandez CO]]
[[Category: Copper protein beta barrel electron transfer]]
[[Category: Luchinat C]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:49:29 2008''
[[Category: Safarov N]]
[[Category: Shumilin S]]
[[Category: Vila AJ]]

Latest revision as of 02:42, 28 December 2023

SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803

Structural highlights

1j5c is a 1 chain structure with sequence from Synechocystis sp. PCC 6803. This structure supersedes the now removed PDB entry 1i0w. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PLAS_SYNY3 Participates in electron transfer between P700 and the cytochrome b6-f complex in photosystem I.[HAMAP-Rule:MF_00566]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Bertini I, Ciurli S, Dikiy A, Fernandez CO, Luchinat C, Safarov N, Shumilin S, Vila AJ. The first solution structure of a paramagnetic copper(II) protein: the case of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803. J Am Chem Soc. 2001 Mar 14;123(10):2405-13. PMID:11456890
Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1j5c&oldid=4006249"