1dw0: Difference between revisions

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<StructureSection load='1dw0' size='340' side='right'caption='[[1dw0]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
<StructureSection load='1dw0' size='340' side='right'caption='[[1dw0]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dw0]] 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=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.82&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dw1|1dw1]], [[1dw2|1dw2]], [[1dw3|1dw3]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [https://pdbe.org/1dw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw0 ProSAT]</span></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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [https://pdbe.org/1dw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SHP_RHOS4 SHP_RHOS4]] High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.  
[https://www.uniprot.org/uniprot/SHP_CERS4 SHP_CERS4] High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1dw0 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=1dw0 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The photosynthetic bacterium Rhodobacter sphaeroides produces a heme protein (SHP), which is an unusual c-type cytochrome capable of transiently binding oxygen during autooxidation. Similar proteins have not only been observed in other photosynthetic bacteria but also in the obligate methylotroph Methylophilus methylotrophus and the metal reducing bacterium Shewanella putrefaciens. A three-dimensional structure of SHP was derived using the multiple isomorphous replacement phasing method. Besides a model for the oxidized state (to 1.82 A resolution), models for the reduced state (2.1 A resolution), the oxidized molecule liganded with cyanide (1. 90 A resolution), and the reduced molecule liganded with nitric oxide (2.20 A resolution) could be derived. The SHP structure represents a new variation of the class I cytochrome c fold. The oxidized state reveals a novel sixth heme ligand, Asn(88), which moves away from the iron upon reduction or when small molecules bind. The distal side of the heme has a striking resemblance to other heme proteins that bind gaseous compounds. In SHP the liberated amide group of Asn(88) stabilizes solvent-shielded ligands through a hydrogen bond.
Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.,Leys D, Backers K, Meyer TE, Hagen WR, Cusanovich MA, Van Beeumen JJ J Biol Chem. 2000 May 26;275(21):16050-6. PMID:10821858<ref>PMID:10821858</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dw0" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Cereibacter sphaeroides]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Rhodobacter sphaeroides]]
[[Category: Backers K]]
[[Category: Backers, K]]
[[Category: Cusanovich MA]]
[[Category: Beeumen, J J.Van]]
[[Category: Hagen WR]]
[[Category: Cusanovich, M A]]
[[Category: Leys D]]
[[Category: Hagen, W R]]
[[Category: Meyer TE]]
[[Category: Leys, D]]
[[Category: Van Beeumen JJ]]
[[Category: Meyer, T E]]
[[Category: Asparagine ligation]]
[[Category: Cytochrome c]]
[[Category: Disulfide bridge]]
[[Category: Oxygen binding]]
[[Category: Oxygen storage-transport complex]]

Revision as of 12:54, 20 March 2024

STRUCTURE OF OXIDIZED SHP, AN OXYGEN BINDING CYTOCHROME CSTRUCTURE OF OXIDIZED SHP, AN OXYGEN BINDING CYTOCHROME C

Structural highlights

1dw0 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 1.82Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SHP_CERS4 High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.

Evolutionary Conservation

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

See Also

1dw0, resolution 1.82Å

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