1wd0: Difference between revisions
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< | ==Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers== | ||
<StructureSection load='1wd0' size='340' side='right'caption='[[1wd0]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1wd0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WD0 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]] 1.9Å</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=1wd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wd0 OCA], [https://pdbe.org/1wd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wd0 RCSB], [https://www.ebi.ac.uk/pdbsum/1wd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wd0 ProSAT]</span></td></tr> | ||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DN7D_SULAC DN7D_SULAC] Can constrain negative DNA supercoils. May be involved in maintaining the integrity of the genome at high temperature.[UniProtKB:P61990] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The protein Sac7d belongs to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Two new crystal forms of Sac7d in complex with the DNA decamers CCTATATAGG and CCTACGTAGG were obtained and their structures were determined by molecular replacement. The refined models yielded R/Rfree values of 0.221/0.257 and 0.248/0.290 at 1.9 and 2.2 A resolution, respectively. The protein structures are similar to the previously determined structure of Sac7d-GCGATCGC (PDB code 1azp), but the DNA molecules are more bent overall, by 14-20 degrees. The relative positions of the Sac7d protein and the bound DNA also differ by rotations of 6-10 degrees and translations of 1.0-2.4 A. In addition to the water molecules in the central cavity, three additional conserved water molecules are found that mediate the protein-DNA interactions. The decamer DNA fragments form virtual double helices in the crystal, with a unit length of eight base pairs. The molecular packing of the new crystal forms differs from that of 1azp. The terminal nucleotides are opened up and form triple base pairs with other DNA molecules. Through lattice contacts, the Sac7d molecule also makes additional interactions with DNA, whereas only limited protein-protein interactions are seen. | |||
Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers.,Ko TP, Chu HM, Chen CY, Chou CC, Wang AH Acta Crystallogr D Biol Crystallogr. 2004 Aug;60(Pt 8):1381-7. Epub 2004, Jul 21. PMID:15272160<ref>PMID:15272160</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1wd0" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
[[Category: | |||
[[Category: Sulfolobus acidocaldarius]] | [[Category: Sulfolobus acidocaldarius]] | ||
[[Category: Chen | [[Category: Chen C-Y]] | ||
[[Category: Chou | [[Category: Chou C-C]] | ||
[[Category: Chu | [[Category: Chu H-M]] | ||
[[Category: Ko | [[Category: Ko T-P]] | ||
[[Category: Wang | [[Category: Wang AH-J]] | ||
Latest revision as of 14:25, 2 August 2023
Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamersCrystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers
Structural highlights
FunctionDN7D_SULAC Can constrain negative DNA supercoils. May be involved in maintaining the integrity of the genome at high temperature.[UniProtKB:P61990] Publication Abstract from PubMedThe protein Sac7d belongs to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Two new crystal forms of Sac7d in complex with the DNA decamers CCTATATAGG and CCTACGTAGG were obtained and their structures were determined by molecular replacement. The refined models yielded R/Rfree values of 0.221/0.257 and 0.248/0.290 at 1.9 and 2.2 A resolution, respectively. The protein structures are similar to the previously determined structure of Sac7d-GCGATCGC (PDB code 1azp), but the DNA molecules are more bent overall, by 14-20 degrees. The relative positions of the Sac7d protein and the bound DNA also differ by rotations of 6-10 degrees and translations of 1.0-2.4 A. In addition to the water molecules in the central cavity, three additional conserved water molecules are found that mediate the protein-DNA interactions. The decamer DNA fragments form virtual double helices in the crystal, with a unit length of eight base pairs. The molecular packing of the new crystal forms differs from that of 1azp. The terminal nucleotides are opened up and form triple base pairs with other DNA molecules. Through lattice contacts, the Sac7d molecule also makes additional interactions with DNA, whereas only limited protein-protein interactions are seen. Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers.,Ko TP, Chu HM, Chen CY, Chou CC, Wang AH Acta Crystallogr D Biol Crystallogr. 2004 Aug;60(Pt 8):1381-7. Epub 2004, Jul 21. PMID:15272160[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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