1kby: Difference between revisions

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[[Image:1kby.gif|left|200px]]


{{Structure
==Structure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin heterodimer==
|PDB= 1kby |SIZE=350|CAPTION= <scene name='initialview01'>1kby</scene>, resolution 2.50&Aring;
<StructureSection load='1kby' size='340' side='right'caption='[[1kby]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SPO:SPHEROIDENE'>SPO</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>
<table><tr><td colspan='2'>[[1kby]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KBY FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SPO:SPHEROIDENE'>SPO</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kby OCA], [https://pdbe.org/1kby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kby RCSB], [https://www.ebi.ac.uk/pdbsum/1kby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kby ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kby OCA], [http://www.ebi.ac.uk/pdbsum/1kby PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kby RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/RCEL_CERSP RCEL_CERSP] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.
 
== Evolutionary Conservation ==
'''Structure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin heterodimer'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/1kby_consurf.spt"</scriptWhenChecked>
Crystals have been obtained of reaction centers of the heterodimer mutant that has significantly different properties than wild type due to the primary donor being formed from both a bacteriochlorophyll and bacteriopheophytin rather than two bacteriochlorophylls as found for wild type. The crystals belong to the trigonal space group P3(1)21 and the structure has been refined to a resolution limit of 2.55 A with an R factor of 19.0%. The electron density maps confirm that a primary donor does indeed contain a bacteriopheophytin due to the His to Leu substitution at M202 that coordinates the corresponding bacteriochlorophyll in wild-type. Other structural changes compared to wild type are relatively minor with the relative orientation and positioning of the two tetrapyrroles forming the primary donor being unchanged within the error. Compared to wild type, the only significant alterations are small shifts of residues M196 to M206, a rotation of the side chain of Ile M206, and the loss of a bound water molecule that in wild-type is hydrogen-bonded to both His M202 and the bacteriochlorophyll monomer on the active branch. Since hydrogen-bonding interactions strongly influence the energies of tetrapyrroles, the loss of the water molecule should result in changes in the energies of the bacteriochlorophyll monomer that contributes to the observed functional differences with wild-type.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
1KBY is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBY OCA].  
</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=1kby ConSurf].
 
<div style="clear:both"></div>
==Reference==
__TOC__
The structure of the heterodimer reaction center from Rhodobacter sphaeroides at 2.55 a resolution., Camara-Artigas A, Magee C, Goetsch A, Allen JP, Photosynth Res. 2002;74(1):87-93. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16228547 16228547]
</StructureSection>
[[Category: Protein complex]]
[[Category: Cereibacter sphaeroides]]
[[Category: Rhodobacter sphaeroides]]
[[Category: Large Structures]]
[[Category: Allen, J P.]]
[[Category: Allen JP]]
[[Category: Camara-Artigas, A.]]
[[Category: Camara-Artigas A]]
[[Category: Goetsch, A.]]
[[Category: Goetsch A]]
[[Category: Magee, C.]]
[[Category: Magee C]]
[[Category: transmembrane alpha helix]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:46:21 2008''

Latest revision as of 10:45, 7 February 2024

Structure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin heterodimerStructure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin heterodimer

Structural highlights

1kby is a 3 chain structure with sequence from Cereibacter sphaeroides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:, , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RCEL_CERSP The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.

Evolutionary Conservation

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

1kby, resolution 2.50Å

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