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2q4c

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Revision as of 08:07, 25 June 2021

Ensemble refinement of the protein crystal structure of annexin from Arabidopsis thaliana gene At1g35720

Structural highlights

2q4c is a 2 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1ycn
Gene:	AT1G35720, ANN1, ANNAT1, ANX23-ATH, ATOXY5, OXY5 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ANXD1_ARATH] Has a peroxidase activity. May act in counteracting oxidative stress. May also mediate regulated, targeted secretion of Golgi-derived vesicles during seedling development.^[1] ^[2]

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^[3]

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

References

↑ Gorecka KM, Konopka-Postupolska D, Hennig J, Buchet R, Pikula S. Peroxidase activity of annexin 1 from Arabidopsis thaliana. Biochem Biophys Res Commun. 2005 Oct 28;336(3):868-75. PMID:16153598 doi:http://dx.doi.org/S0006-291X(05)01903-0
↑ Clark GB, Lee D, Dauwalder M, Roux SJ. Immunolocalization and histochemical evidence for the association of two different Arabidopsis annexins with secretion during early seedling growth and development. Planta. 2005 Feb;220(4):621-31. Epub 2004 Sep 11. PMID:15368128 doi:http://dx.doi.org/10.1007/s00425-004-1374-7
↑ 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 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q4c"

@@ Line 1: / Line 1: @@
 ==Ensemble refinement of the protein crystal structure of annexin from Arabidopsis thaliana gene At1g35720==
-<StructureSection load='2q4c' size='340' side='right' caption='[[2q4c]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
+<StructureSection load='2q4c' size='340' side='right'caption='[[2q4c]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q4c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q4C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q4c]] is a 2 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=2Q4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4C FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ycn|1ycn]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ycn|1ycn]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT1G35720, ANN1, ANNAT1, ANX23-ATH, ATOXY5, OXY5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT1G35720, ANN1, ANNAT1, ANX23-ATH, ATOXY5, OXY5 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4c OCA], [http://pdbe.org/2q4c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q4c RCSB], [http://www.ebi.ac.uk/pdbsum/2q4c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4c ProSAT]</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=2q4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4c OCA], [https://pdbe.org/2q4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4c RCSB], [https://www.ebi.ac.uk/pdbsum/2q4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4c ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ANXD1_ARATH ANXD1_ARATH]] Has a peroxidase activity. May act in counteracting oxidative stress. May also mediate regulated, targeted secretion of Golgi-derived vesicles during seedling development.<ref>PMID:16153598</ref> <ref>PMID:15368128</ref>
+[[https://www.uniprot.org/uniprot/ANXD1_ARATH ANXD1_ARATH]] Has a peroxidase activity. May act in counteracting oxidative stress. May also mediate regulated, targeted secretion of Golgi-derived vesicles during seedling development.<ref>PMID:16153598</ref> <ref>PMID:15368128</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Annexin|Annexin]]
+*[[Annexin 3D structures|Annexin 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 37: @@
 </StructureSection>
 [[Category: Arath]]
+[[Category: Large Structures]]
 [[Category: Structural genomic]]
 [[Category: Kondrashov, D A]]

2q4c

From Proteopedia

Revision as of 08:07, 25 June 2021

Ensemble refinement of the protein crystal structure of annexin from Arabidopsis thaliana gene At1g35720

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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