2v1e: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:2v1e.gif|left|200px]]
- {{Structure
+==Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 6.8==
-|PDB= 2v1e |SIZE=350|CAPTION= <scene name='initialview01'>2v1e</scene>, resolution 1.30&Aring;
+<StructureSection load='2v1e' size='340' side='right'caption='[[2v1e]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Hem+Binding+Site+For+Residue+A+1154'>AC1</scene>, <scene name='pdbsite=AC2:Hyd+Binding+Site+For+Residue+A+1155'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+A+1156'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+A+1157'>AC4</scene>, <scene name='pdbsite=AC5:Gol+Binding+Site+For+Residue+A+1158'>AC5</scene>, <scene name='pdbsite=AC6:Gol+Binding+Site+For+Residue+A+1159'>AC6</scene> and <scene name='pdbsite=AC7:Gol+Binding+Site+For+Residue+A+1160'>AC7</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HYD:HYDROXY+GROUP'>HYD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[2v1e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V1E 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]] 1.3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2v1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v1e OCA], [https://pdbe.org/2v1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v1e RCSB], [https://www.ebi.ac.uk/pdbsum/2v1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v1e ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1azi|1AZI]], [[1bje|1BJE]], [[1dwr|1DWR]], [[1dws|1DWS]], [[1dwt|1DWT]], [[1gjn|1GJN]], [[1hrm|1HRM]], [[1hsy|1HSY]], [[1npf|1NPF]], [[1npg|1NPG]], [[1nz2|1NZ2]], [[1nz3|1NZ3]], [[1nz4|1NZ4]], [[1nz5|1NZ5]], [[1rse|1RSE]], [[1wla|1WLA]], [[1xch|1XCH]], [[1yma|1YMA]], [[1ymb|1YMB]], [[1ymc|1YMC]], [[2frf|2FRF]], [[2fri|2FRI]], [[2frj|2FRJ]], [[2frk|2FRK]], [[2in4|2IN4]], [[2v1f|2V1F]], [[2v1g|2V1G]], [[2v1h|2V1H]], [[2v1i|2V1I]], [[2v1j|2V1J]], [[2v1k|2V1K]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v1e OCA], [http://www.ebi.ac.uk/pdbsum/2v1e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2v1e RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/MYG_HORSE MYG_HORSE] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
+== 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/v1/2v1e_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=2v1e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (&lt;1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe-O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an Fe(IV)-O species with a single bond. The presence of Fe(IV) is indicated by a small isomer shift of delta = 0.07 mm/s from Mossbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.
-'''CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II- INTERMEDIATE H AT PH 6.8'''
+Crystallographic and spectroscopic studies of peroxide-derived myoglobin compound II and occurrence of protonated FeIV O.,Hersleth HP, Uchida T, Rohr AK, Teschner T, Schunemann V, Kitagawa T, Trautwein AX, Gorbitz CH, Andersson KK J Biol Chem. 2007 Aug 10;282(32):23372-86. Epub 2007 Jun 12. PMID:17565988<ref>PMID:17565988</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2v1e" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (&lt;1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe-O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an Fe(IV)-O species with a single bond. The presence of Fe(IV) is indicated by a small isomer shift of delta = 0.07 mm/s from Mossbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.
+*[[Myoglobin 3D structures|Myoglobin 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-V1E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V1E OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Crystallographic and spectroscopic studies of peroxide-derived myoglobin compound II and occurrence of protonated FeIV O., Hersleth HP, Uchida T, Rohr AK, Teschner T, Schunemann V, Kitagawa T, Trautwein AX, Gorbitz CH, Andersson KK, J Biol Chem. 2007 Aug 10;282(32):23372-86. Epub 2007 Jun 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17565988 17565988]
 [[Category: Equus caballus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Andersson, K K.]]
+[[Category: Andersson KK]]
-[[Category: Gorbitz, C H.]]
+[[Category: Gorbitz CH]]
-[[Category: Hersleth, H P.]]
+[[Category: Hersleth H-P]]
-[[Category: ferryl]]
-[[Category: haem]]
-[[Category: heme]]
-[[Category: hydroxy radical]]
-[[Category: iron]]
-[[Category: metal-binding]]
-[[Category: monooxygenase]]
-[[Category: muscle protein]]
-[[Category: oxygen activation]]
-[[Category: oxygen transport]]
-[[Category: peroxidase]]
-[[Category: reaction intermediate]]
-[[Category: transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:07:24 2008''