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1vrf

From Proteopedia

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{{Seed}}
 
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[[Image:1vrf.png|left|200px]]
 
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==SOLUTION STRUCTURE OF COMPONENT IV GLYCERA DIBRANCHIATA MONOMERIC HEMOGLOBIN-CO==
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The line below this paragraph, containing "STRUCTURE_1vrf", creates the "Structure Box" on the page.
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<StructureSection load='1vrf' size='340' side='right'caption='[[1vrf]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1vrf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycera_dibranchiata Glycera dibranchiata]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VRF FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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></td></tr>
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{{STRUCTURE_1vrf| PDB=1vrf | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vrf OCA], [https://pdbe.org/1vrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vrf RCSB], [https://www.ebi.ac.uk/pdbsum/1vrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vrf ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GLB4_GLYDI GLB4_GLYDI]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vr/1vrf_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1vrf ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The solution structure and backbone dynamics of the recombinant, ferrous CO-ligated form of component IV monomeric hemoglobin from Glycera dibranchiata (GMH4CO) have been characterized by NMR spectroscopy. Distance geometry and simulated annealing calculations utilizing a total of 2550 distance and torsion angle constraints yielded an ensemble of 29 structures with an overall average backbone rmsd of 0.48 A from the average structure. Differences between the solution structure and a related crystal structure are confined to regions of lower precision in either the NMR or X-ray structure, or in regions where the amino acid sequences differ. 15N relaxation measurements at 76.0 and 60.8 MHz were analyzed with an extended model-free approach, and revealed low-frequency motions in the vicinity of the heme, concentrated in the F helix. Amide proton protection factors were obtained from H-D amide exchange measurements on 15N-labeled protein. Patterns in the backbone dynamics and protection factors were shown to correlate with regions of heterogeneity and disorder in the ensemble of NMR structures and with large crystallographic B-factors in the X-ray structures. Surprisingly, while the backbone atoms of the F helix have higher rmsds and larger measures of dynamics on the microsecond to millisecond time scale than the other helices, amide protection factors for residues in the F helix were observed to be similar to those of the other helices. This contrasts with H-D amide exchange measurements on sperm whale myoglobin which indicated low protection for the F helix (S. N. Loh and B. F. Volkman, unpublished results). These results for GMH4 suggest a model in which the F helix undergoes collective motions as a relatively rigid hydrogen-bonded unit, possibly pivoting about a central position near residue Val87.
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===SOLUTION STRUCTURE OF COMPONENT IV GLYCERA DIBRANCHIATA MONOMERIC HEMOGLOBIN-CO===
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Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO.,Volkman BF, Alam SL, Satterlee JD, Markley JL Biochemistry. 1998 Aug 4;37(31):10906-19. PMID:9692983<ref>PMID:9692983</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1vrf" style="background-color:#fffaf0;"></div>
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<!--
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_9692983}}, adds the Publication Abstract to the page
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*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 9692983 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_9692983}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1VRF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Glycera_dibranchiata Glycera dibranchiata]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRF OCA].
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==Reference==
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Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO., Volkman BF, Alam SL, Satterlee JD, Markley JL, Biochemistry. 1998 Aug 4;37(31):10906-19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9692983 9692983]
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[[Category: Glycera dibranchiata]]
[[Category: Glycera dibranchiata]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Alam, S L.]]
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[[Category: Alam SL]]
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[[Category: Markley, J L.]]
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[[Category: Markley JL]]
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[[Category: Satterlee, J D.]]
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[[Category: Satterlee JD]]
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[[Category: Volkman, B F.]]
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[[Category: Volkman BF]]
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[[Category: Globin]]
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[[Category: Heme protein]]
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[[Category: Oxygen transport]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 13:19:53 2008''
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Current revision

SOLUTION STRUCTURE OF COMPONENT IV GLYCERA DIBRANCHIATA MONOMERIC HEMOGLOBIN-CO

PDB ID 1vrf

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