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2q50

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Ensemble refinement of the protein crystal structure of a glyoxylate/hydroxypyruvate reductase from Homo sapiens

Structural highlights

2q50 is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.45Å, 8 models
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

GRHPR_HUMAN Defects in GRHPR are the cause of hyperoxaluria primary type 2 (HP2) [MIM:260000; also known as primary hyperoxaluria type II (PH2). HP2 is a disorder where the main clinical manifestation is calcium oxalate nephrolithiasis though chronic as well as terminal renal insufficiency has been described. It is characterized by an elevated urinary excretion of oxalate and L-glycerate.^[1]

Function

GRHPR_HUMAN Enzyme with hydroxy-pyruvate reductase, glyoxylate reductase and D-glycerate dehydrogenase enzymatic activities. Reduces hydroxypyruvate to D-glycerate, glyoxylate to glycolate oxidizes D-glycerate to hydroxypyruvate.

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 PubMed

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.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Cramer SD, Ferree PM, Lin K, Milliner DS, Holmes RP. The gene encoding hydroxypyruvate reductase (GRHPR) is mutated in patients with primary hyperoxaluria type II. Hum Mol Genet. 1999 Oct;8(11):2063-9. PMID:10484776
↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q50"

@@ Line 3: / Line 3: @@
 <StructureSection load='2q50' size='340' side='right'caption='[[2q50]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q50]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q50 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q50 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q50]] is a 4 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=2Q50 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q50 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;, 8 models</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2h1s|2h1s]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GRHPR, GLXR, MSTP035 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glyoxylate_reductase_(NADP(+)) Glyoxylate reductase (NADP(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.79 1.1.1.79] </span></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=2q50 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q50 OCA], [https://pdbe.org/2q50 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q50 RCSB], [https://www.ebi.ac.uk/pdbsum/2q50 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q50 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/GRHPR_HUMAN GRHPR_HUMAN]] Defects in GRHPR are the cause of hyperoxaluria primary type 2 (HP2) [MIM:[https://omim.org/entry/260000 260000]]; also known as primary hyperoxaluria type II (PH2). HP2 is a disorder where the main clinical manifestation is calcium oxalate nephrolithiasis though chronic as well as terminal renal insufficiency has been described. It is characterized by an elevated urinary excretion of oxalate and L-glycerate.<ref>PMID:10484776</ref>
+[https://www.uniprot.org/uniprot/GRHPR_HUMAN GRHPR_HUMAN] Defects in GRHPR are the cause of hyperoxaluria primary type 2 (HP2) [MIM:[https://omim.org/entry/260000 260000]; also known as primary hyperoxaluria type II (PH2). HP2 is a disorder where the main clinical manifestation is calcium oxalate nephrolithiasis though chronic as well as terminal renal insufficiency has been described. It is characterized by an elevated urinary excretion of oxalate and L-glycerate.<ref>PMID:10484776</ref>
 == Function ==
-[[https://www.uniprot.org/uniprot/GRHPR_HUMAN GRHPR_HUMAN]] Enzyme with hydroxy-pyruvate reductase, glyoxylate reductase and D-glycerate dehydrogenase enzymatic activities. Reduces hydroxypyruvate to D-glycerate, glyoxylate to glycolate oxidizes D-glycerate to hydroxypyruvate.
+[https://www.uniprot.org/uniprot/GRHPR_HUMAN GRHPR_HUMAN] Enzyme with hydroxy-pyruvate reductase, glyoxylate reductase and D-glycerate dehydrogenase enzymatic activities. Reduces hydroxypyruvate to D-glycerate, glyoxylate to glycolate oxidizes D-glycerate to hydroxypyruvate.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / Line 17: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q5/2q50_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 37: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Structural genomic]]
+[[Category: Kondrashov DA]]
-[[Category: Kondrashov, D A]]
+[[Category: Levin EJ]]
-[[Category: Levin, E J]]
+[[Category: Phillips Jr GN]]
-[[Category: Phillips, G N]]
+[[Category: Wesenberg GE]]
-[[Category: Wesenberg, G E]]
-[[Category: Cesg]]
-[[Category: Ensemble refinement]]
-[[Category: Glyoxylate reductase]]
-[[Category: Hydroxypyruvate reductase]]
-[[Category: Oxidoreductase]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Q9ubq7]]
-[[Category: Refinement methodology development]]

2q50

From Proteopedia

Current revision

Ensemble refinement of the protein crystal structure of a glyoxylate/hydroxypyruvate reductase from Homo sapiens

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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