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2q40

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Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g17340

Structural highlights

2q40 is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

D89S2_ARATH Metal-dependent phosphatase with probable damage-control functions (PubMed:27322068). Shows phosphatase activity against several substrates, including sugar phosphates and p-nitrophenyl phosphate(pNPP) (PubMed:27322068). Prefers sugar phosphate substrates, including the extremely potent glycating agents ribose-5-phosphate and erythrose-4-phosphate (PubMed:27322068).^[1]

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

↑ Huang L, Khusnutdinova A, Nocek B, Brown G, Xu X, Cui H, Petit P, Flick R, Zallot R, Balmant K, Ziemak MJ, Shanklin J, de Crecy-Lagard V, Fiehn O, Gregory JF 3rd, Joachimiak A, Savchenko A, Yakunin AF, Hanson AD. A family of metal-dependent phosphatases implicated in metabolite damage-control. Nat Chem Biol. 2016 Jun 20. doi: 10.1038/nchembio.2108. PMID:27322068 doi:http://dx.doi.org/10.1038/nchembio.2108
↑ 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 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q40"

@@ Line 3: / Line 3: @@
 <StructureSection load='2q40' size='340' side='right'caption='[[2q40]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q40]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q40 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q40]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q40 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xfi|1xfi]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At2g17340, F5J6.10 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2q40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q40 OCA], [https://pdbe.org/2q40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q40 RCSB], [https://www.ebi.ac.uk/pdbsum/2q40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q40 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/D89S2_ARATH D89S2_ARATH] Metal-dependent phosphatase with probable damage-control functions (PubMed:27322068). Shows phosphatase activity against several substrates, including sugar phosphates and p-nitrophenyl phosphate(pNPP) (PubMed:27322068). Prefers sugar phosphate substrates, including the extremely potent glycating agents ribose-5-phosphate and erythrose-4-phosphate (PubMed:27322068).<ref>PMID:27322068</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[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: At2g17340]]
-[[Category: Cesg]]
-[[Category: Ensemble refinement]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Refinement methodology development]]
-[[Category: Unknown function]]

2q40

From Proteopedia

Current revision

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g17340

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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