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5ezf

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Racemic crystal structures of Pribnow box consensus promoter sequence (Pbca)

Structural highlights

5ezf is a 2 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.65Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods-that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence 'TATAAT'. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65-2.3 A), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence.

Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography.,Mandal PK, Collie GW, Srivastava SC, Kauffmann B, Huc I Nucleic Acids Res. 2016 May 2. pii: gkw367. PMID:27137886^[1]

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

References

↑ Mandal PK, Collie GW, Srivastava SC, Kauffmann B, Huc I. Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. Nucleic Acids Res. 2016 May 2. pii: gkw367. PMID:27137886 doi:http://dx.doi.org/10.1093/nar/gkw367

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ezf"

@@ Line 3: / Line 3: @@
 <StructureSection load='5ezf' size='340' side='right'caption='[[5ezf]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ezf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EZF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EZF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ezf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EZF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.65&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5et9|5et9]], [[5ewb|5ewb]], [[5eyq|5eyq]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ezf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ezf OCA], [http://pdbe.org/5ezf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ezf RCSB], [http://www.ebi.ac.uk/pdbsum/5ezf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ezf 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=5ezf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ezf OCA], [https://pdbe.org/5ezf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ezf RCSB], [https://www.ebi.ac.uk/pdbsum/5ezf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ezf ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 22: / Line 22: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Collie, G W]]
+[[Category: Synthetic construct]]
-[[Category: Huc, I]]
+[[Category: Collie GW]]
-[[Category: Kauffmann, B]]
+[[Category: Huc I]]
-[[Category: Mandal, P K]]
+[[Category: Kauffmann B]]
-[[Category: Srivastava, S C]]
+[[Category: Mandal PK]]
-[[Category: 10 element]]
+[[Category: Srivastava SC]]
-[[Category: B-dna double helix]]
-[[Category: Dna]]
-[[Category: Dna double helix]]
-[[Category: Pribnow box consensus sequence]]
-[[Category: Transcription initiation]]

5ezf

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Current revision

Racemic crystal structures of Pribnow box consensus promoter sequence (Pbca)

Structural highlights

Publication Abstract from PubMed

References

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