2q4r

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[[Image:2q4r.png|left|200px]]
 
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==Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)==
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The line below this paragraph, containing "STRUCTURE_2q4r", creates the "Structure Box" on the page.
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<StructureSection load='2q4r' size='340' side='right'caption='[[2q4r]], [[Resolution|resolution]] 2.09&Aring;' 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'>[[2q4r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4R 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">X-ray diffraction, [[Resolution|Resolution]] 2.09&#8491;, 16 models</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_2q4r| PDB=2q4r | 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=2q4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4r OCA], [https://pdbe.org/2q4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4r RCSB], [https://www.ebi.ac.uk/pdbsum/2q4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4r ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN] Defects in PMM2 are the cause of congenital disorder of glycosylation type 1A (CDG1A) [MIM:[https://omim.org/entry/212065 212065]; also known as carbohydrate-deficient glycoprotein syndrome type Ia (CDGS1A) or Jaeken syndrome. Congenital disorders of glycosylation are metabolic deficiencies in glycoprotein biosynthesis that usually cause severe mental and psychomotor retardation. They are characterized by under-glycosylated serum glycoproteins. CDG1A is an autosomal recessive disorder characterized by a severe encephalopathy with axial hypotonia, abnormal eye movement, and pronounced psychomotor retardation, as well as peripheral neuropathy, cerebellar hypoplasia, and retinitis pigmentosa. Patients show a peculiar distribution of subcutaneous fat, nipple retraction, and hypogonadism.<ref>PMID:9140401</ref> <ref>PMID:9497260</ref> <ref>PMID:9781039</ref> <ref>PMID:10066032</ref> <ref>PMID:10602363</ref> <ref>PMID:10571956</ref> <ref>PMID:11058895</ref> <ref>PMID:11058896</ref> <ref>PMID:10801058</ref> <ref>PMID:11350185</ref> <ref>PMID:12357336</ref> <ref>PMID:15844218</ref> <ref>PMID:17307006</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN] Involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions (By similarity).
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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/q4/2q4r_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2q4r 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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X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.
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===Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)===
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Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744<ref>PMID:17850744</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 2q4r" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17850744}}, adds the Publication Abstract to the page
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*[[Phosphomannomutase|Phosphomannomutase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17850744 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17850744}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[2q4r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4R OCA].
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==Reference==
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<ref group="xtra">PMID:017850744</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Phosphomannomutase]]
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[[Category: Large Structures]]
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[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
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[[Category: Kondrashov DA]]
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[[Category: Kondrashov, D A.]]
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[[Category: Levin EJ]]
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[[Category: Levin, E J.]]
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[[Category: Phillips Jr GN]]
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[[Category: Phillips, G N.]]
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[[Category: Wesenberg GE]]
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[[Category: Wesenberg, G E.]]
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[[Category: Bc008310]]
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[[Category: Carbohydrate-deficient glycoprotein syndrome]]
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[[Category: Center for eukaryotic structural genomic]]
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[[Category: Cesg]]
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[[Category: Ensemble refinement]]
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[[Category: Had superfamily]]
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[[Category: Hs 313504]]
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[[Category: Hs 459855]]
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[[Category: Isomerase]]
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[[Category: Jaecken disease]]
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[[Category: Pfam pf03332]]
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[[Category: Phosphatase]]
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[[Category: Protein structure initiative]]
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[[Category: Psi]]
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[[Category: Refinement methodology development]]
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[[Category: Structural genomic]]
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Current revision

Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)

PDB ID 2q4r

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OCA

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