2hbg: Difference between revisions

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New page: left|200px<br /> <applet load="2hbg" size="450" color="white" frame="true" align="right" spinBox="true" caption="2hbg, resolution 1.5Å" /> '''GLYCERA DIBRANCHIATA...
 
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[[Image:2hbg.gif|left|200px]]<br />
<applet load="2hbg" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2hbg, resolution 1.5&Aring;" />
'''GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTION'''<br />


==Overview==
==GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTION==
The coelomic cells of the common marine bloodworm Glycera dibranchiata, contain several hemoglobin monomers and polydisperse polymers. We present, the refined structure of one of the Glycera monomers at 1.5 A resolution., The molecular model for protein and ordered solvent for the deoxy form of, the Glycera monomer has been refined to a crystallographic R-factor of, 12.7% against an X-ray diffraction dataset at 1.5 A resolution. The, positions of 1095 protein atoms have been determined with a maximum, root-mean-square (r.m.s.) error of 0.13 A, and the r.m.s. deviation from, ideal bond lengths is 0.015 A and from ideal bond angles is 1.0 degree., The r.m.s. deviation of planar groups from their least-squares planes is, 0.007 A, and the r.m.s. deviation for torsion angles is 1.2 degrees for, peptide groups and 16.8 degrees for side-chains. A total of 153 water, molecules has been located, and they have been refined to a final average, occupancy of 0.80. Multiple conformations have been found for five, side-chains, and a change has been suggested for the sequence at five, residues. The heme group is present in the "reverse" orientation that, differs only in the positions of the vinyl beta-carbons from the "normal", orientation. The doming of the heme towards the proximal side, and the, bond distances and angles of the heme and proximal histidine are typical, of most deoxy globin structures. The substitution of leucine for the, distal histidine residue (E7) creates an unusually hydrophobic heme, pocket.
<StructureSection load='2hbg' size='340' side='right'caption='[[2hbg]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2hbg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycera_dibranchiata Glycera dibranchiata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HBG FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=2hbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbg OCA], [https://pdbe.org/2hbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hbg RCSB], [https://www.ebi.ac.uk/pdbsum/2hbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbg ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GLB1_GLYDI GLB1_GLYDI]
== 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/hb/2hbg_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=2hbg ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2HBG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Glycera_dibranchiata Glycera dibranchiata] with HEM as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2HBG OCA].
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Glycera dibranchiata hemoglobin. Structure and refinement at 1.5 A resolution., Arents G, Love WE, J Mol Biol. 1989 Nov 5;210(1):149-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2585515 2585515]
[[Category: Glycera dibranchiata]]
[[Category: Glycera dibranchiata]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Arents, G.A.]]
[[Category: Arents GA]]
[[Category: Love, W.E.]]
[[Category: Love WE]]
[[Category: HEM]]
[[Category: oxygen transport]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov  8 13:31:38 2007''

Latest revision as of 12:31, 14 February 2024

GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTIONGLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTION

Structural highlights

2hbg is a 1 chain structure with sequence from Glycera dibranchiata. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLB1_GLYDI

Evolutionary Conservation

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

See Also

2hbg, resolution 1.50Å

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