3ov8: Difference between revisions
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The entry 3ov8 is | ==Crystal structure of AF1382 from Archaeoglobus fulgidus, High resolution== | ||
<StructureSection load='3ov8' size='340' side='right'caption='[[3ov8]], [[Resolution|resolution]] 1.85Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ov8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OV8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OV8 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8501Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=3ov8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ov8 OCA], [https://pdbe.org/3ov8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ov8 RCSB], [https://www.ebi.ac.uk/pdbsum/3ov8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ov8 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Y1382_ARCFU Y1382_ARCFU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 A wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent a novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (DeltaF(anom)/F) of 1.39% for 1.9 A wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360 degrees data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R(free) = 26.8%) to 2.3 A resolution (PDB entry 3o3k). High-resolution data were subsequently collected from a better diffracting crystal using 0.97 A wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R(free) = 21.4%) to 1.85 A resolution (PDB entry 3ov8). AF1382 has a winged-helix-turn-helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1-82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection. | |||
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.,Zhu JY, Fu ZQ, Chen L, Xu H, Chrzas J, Rose J, Wang BC Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1242-52. Epub 2012 Aug 18. PMID:22948926<ref>PMID:22948926</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ov8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Archaeoglobus fulgidus]] | |||
[[Category: Large Structures]] | |||
[[Category: Chang J]] | |||
[[Category: Chen L]] | |||
[[Category: Fu Z-Q]] | |||
[[Category: Hao X]] | |||
[[Category: Rose JP]] | |||
[[Category: Wang BC]] | |||
[[Category: Yang H]] | |||
[[Category: Zhao M]] | |||
[[Category: Zhu J-Y]] | |||