2hbg: Difference between revisions
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==GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTION== | ==GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTION== | ||
<StructureSection load='2hbg' size='340' side='right' caption='[[2hbg]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='2hbg' size='340' side='right' caption='[[2hbg]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
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<table><tr><td colspan='2'>[[2hbg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bloodworm Bloodworm]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HBG FirstGlance]. <br> | <table><tr><td colspan='2'>[[2hbg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bloodworm Bloodworm]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HBG FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbg OCA], [http://pdbe.org/2hbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hbg RCSB], [http://www.ebi.ac.uk/pdbsum/2hbg PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbg OCA], [http://pdbe.org/2hbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hbg RCSB], [http://www.ebi.ac.uk/pdbsum/2hbg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbg ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
Revision as of 10:07, 29 November 2017
GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTIONGLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTION
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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:2585515[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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