This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2q4f

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Ensemble refinement of the crystal structure of putative histidine-containing phosphotransfer protein from rice, Ak104879

Structural highlights

2q4f is a 2 chain structure with sequence from Oryza sativa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OHP2_ORYSJ Functions as two-component phosphorelay mediators between cytokinin sensor histidine kinases and response regulators (B-type ARRs). Plays an important role in propagating cytokinin signal transduction through the multistep His-to-Asp phosphorelay (By similarity). Functions as positive regulator of the cytokinin signaling pathway. May play a regulatory role in salt and drought tolerance during plant development (PubMed:24578505).[UniProtKB:Q8L9T7]^[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

↑ Sun L, Zhang Q, Wu J, Zhang L, Jiao X, Zhang S, Zhang Z, Sun D, Lu T, Sun Y. Two rice authentic histidine phosphotransfer proteins, OsAHP1 and OsAHP2, mediate cytokinin signaling and stress responses in rice. Plant Physiol. 2014 May;165(1):335-45. doi: 10.1104/pp.113.232629. Epub 2014 Feb , 27. PMID:24578505 doi:http://dx.doi.org/10.1104/pp.113.232629
↑ 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/2q4f"

@@ Line 3: / Line 3: @@
 <StructureSection load='2q4f' size='340' side='right'caption='[[2q4f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q4f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Orysa Orysa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q4f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4F FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yvi|1yvi]]</div></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&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HP1, AK104879, Os09g0567400, LOC_Os09g39400, OJ1155_H10.30 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4530 ORYSA])</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=2q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4f OCA], [https://pdbe.org/2q4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4f RCSB], [https://www.ebi.ac.uk/pdbsum/2q4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4f ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/OHP2_ORYSJ OHP2_ORYSJ] Functions as two-component phosphorelay mediators between cytokinin sensor histidine kinases and response regulators (B-type ARRs). Plays an important role in propagating cytokinin signal transduction through the multistep His-to-Asp phosphorelay (By similarity). Functions as positive regulator of the cytokinin signaling pathway. May play a regulatory role in salt and drought tolerance during plant development (PubMed:24578505).[UniProtKB:Q8L9T7]<ref>PMID:24578505</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 33: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Orysa]]
+[[Category: Oryza sativa]]
-[[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: Ak104879]]
-[[Category: Cesg]]
-[[Category: Ensemble refinement]]
-[[Category: Hp1]]
-[[Category: Phosphorelay mediator]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Refinement methodology development]]
-[[Category: Signaling protein]]

2q4f

From Proteopedia

Current revision

Ensemble refinement of the crystal structure of putative histidine-containing phosphotransfer protein from rice, Ak104879

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox