3pmg: Difference between revisions
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New page: left|200px<br /><applet load="3pmg" size="450" color="white" frame="true" align="right" spinBox="true" caption="3pmg, resolution 2.4Å" /> '''STRUCTURE OF RABBIT M... |
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== | ==STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY== | ||
Data between 6.0 and 2.4 A resolution, collected at 253 K, wer used to | <StructureSection load='3pmg' size='340' side='right'caption='[[3pmg]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3pmg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pmg 2pmg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PMG FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglucomutase Phosphoglucomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.2 5.4.2.2] </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=3pmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pmg OCA], [http://pdbe.org/3pmg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pmg RCSB], [http://www.ebi.ac.uk/pdbsum/3pmg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pmg ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/PGM1_RABIT PGM1_RABIT]] This enzyme participates in both the breakdown and synthesis of glucose. | |||
== 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/pm/3pmg_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=3pmg ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Data between 6.0 and 2.4 A resolution, collected at 253 K, wer used to refine a revised atomic model of muscle phosphoglucomutase: final crystallographic R factor = 16.3% (Rfree = 19.1%); final r.m.s. deviations from ideal bond lengths and angles = 0.018 A and 3.2 degrees, respectively. Features of the protein that were recognized only in the revised model include: the disposition of water molecules within domain-domain interfaces; two ion pairs buried in domain-domain interfaces, one of which is a structural arginine around which the active-site phosphoserine loop is wound; the basic architecture of the active-site 'crevice', which is a groove in a 1(1/3)-turn helix, open at both ends, that is produced by the interfacing of the four domains; the distorted hexacoordinate ligand sphere of the active-site Mg2+, where the enzymic phosphate group acts as a bidentate ligand; a pair of arginine residues in domain IV that form part of the enzymic phosphate-binding site (distal subsite) whose disposition in the two monomers of the asymmetric unit is affected unequally by distant crystallographic contacts; structural differences throughout domain IV, produced by these differing contacts, that may mimic solution differences induced by substrate binding; large differences in individually refined Debye-Waller thermal factors for corresponding main-chain atoms in monomers (1) and (2), suggesting a dynamic disorder within the crystal that may involve domain-size groups of residues; and a 'nucleophilic elbow' in the active site that resides in a topological environment differing from previous descriptions of this type of structure in other proteins. | |||
Structure of rabbit muscle phosphoglucomutase refined at 2.4 A resolution.,Liu Y, Ray WJ Jr, Baranidharan S Acta Crystallogr D Biol Crystallogr. 1997 Jul 1;53(Pt 4):392-405. PMID:15299905<ref>PMID:15299905</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3pmg" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Oryctolagus cuniculus]] | [[Category: Oryctolagus cuniculus]] | ||
[[Category: Phosphoglucomutase]] | [[Category: Phosphoglucomutase]] | ||
[[Category: Baranidharan, S]] | |||
[[Category: Baranidharan, S | [[Category: Junior, W J.Ray]] | ||
[[Category: Junior, W | [[Category: Liu, Y]] | ||
[[Category: Liu, Y | [[Category: Isomerase]] | ||
[[Category: | [[Category: Phosphotransferase]] | ||
[[Category: | |||
