1dxc: Difference between revisions

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<StructureSection load='1dxc' size='340' side='right'caption='[[1dxc]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='1dxc' size='340' side='right'caption='[[1dxc]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dxc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phymc Phymc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DXC FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dxc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DXC FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.4&#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;'>[[1dxd|1dxd]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1dxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dxc OCA], [https://pdbe.org/1dxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dxc RCSB], [https://www.ebi.ac.uk/pdbsum/1dxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dxc 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=1dxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dxc OCA], [https://pdbe.org/1dxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dxc RCSB], [https://www.ebi.ac.uk/pdbsum/1dxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dxc ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.  
[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
== 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=1dxc 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=1dxc ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu-(B10)--&gt;Tyr; His(E7)--&gt;Gln; Thr(E10)--&gt;Arg] to 1.4-A resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to photolysis of the Fe-CO bond, and migration of the photolyzed carbon monoxide (CO*) to a niche in the protein 8.1 A from the heme iron; this cavity corresponds to that hosting an atom of Xe when the crystal is equilibrated with xenon gas at 7 atmospheres [Tilton, R. F., Jr., Kuntz, I. D. &amp; Petsko, G. A. (1984) Biochemistry 23, 2849-2857]. The site occupied by CO* corresponds to that predicted by molecular dynamics simulations previously carried out to account for the NO geminate rebinding of Mb-YQR observed in laser photolysis experiments at room temperature. This secondary docking site differs from the primary docking site identified by previous crystallographic studies on the photolyzed intermediate of wild-type sperm whale Mb performed at cryogenic temperatures [Teng et al. (1994) Nat. Struct. Biol. 1, 701-705] and room temperature [Srajer et al. (1996) Science 274, 1726-1729]. Our experiment shows that the pathway of a small molecule in its trajectory through a protein may be modified by site-directed mutagenesis, and that migration within the protein matrix to the active site involves a limited number of pre-existing cavities identified in the interior space of the protein.
The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin.,Brunori M, Vallone B, Cutruzzola F, Travaglini-Allocatelli C, Berendzen J, Chu K, Sweet RM, Schlichting I Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2058-63. PMID:10681426<ref>PMID:10681426</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dxc" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Phymc]]
[[Category: Physeter catodon]]
[[Category: Berendzen, J]]
[[Category: Berendzen J]]
[[Category: Brunori, M]]
[[Category: Brunori M]]
[[Category: Chu, K]]
[[Category: Chu K]]
[[Category: Cutruzzola, F]]
[[Category: Cutruzzola F]]
[[Category: Schlichting, I]]
[[Category: Schlichting I]]
[[Category: Sweet, R M]]
[[Category: Sweet RM]]
[[Category: Travaglini-Allocatelli, C]]
[[Category: Travaglini-Allocatelli C]]
[[Category: Vallone, B]]
[[Category: Vallone B]]
[[Category: Co complex]]
[[Category: Oxygen storage]]
[[Category: Respiratory protein]]

Revision as of 12:55, 20 March 2024

CO complex of Myoglobin Mb-YQR at 100KCO complex of Myoglobin Mb-YQR at 100K

Structural highlights

1dxc is a 1 chain structure with sequence from Physeter catodon. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MYG_PHYMC Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.

Evolutionary Conservation

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

See Also

1dxc, resolution 1.40Å

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