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.


4hd5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:48, 3 April 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal Structure of BC0361, a polysaccharide deacetylase from Bacillus cereus==
==Crystal Structure of BC0361, a polysaccharide deacetylase from Bacillus cereus==
-
<StructureSection load='4hd5' size='340' side='right' caption='[[4hd5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+
<StructureSection load='4hd5' size='340' side='right'caption='[[4hd5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4hd5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus_atcc_14579 Bacillus cereus atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HD5 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4hd5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_ATCC_14579 Bacillus cereus ATCC 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HD5 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.9&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXU:2-HYDROXY-L-PROLINE'>PXU</scene></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=PXU:2-HYDROXY-L-PROLINE'>PXU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BC0361, BC_0361 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226900 Bacillus cereus ATCC 14579])</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=4hd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hd5 OCA], [https://pdbe.org/4hd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hd5 RCSB], [https://www.ebi.ac.uk/pdbsum/4hd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hd5 ProSAT]</span></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=4hd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hd5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hd5 RCSB], [http://www.ebi.ac.uk/pdbsum/4hd5 PDBsum]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q81IM3_BACCR Q81IM3_BACCR]
-
The structure of BC0361, a polysaccharide deacetylase from Bacillus cereus, has been determined using an unconventional molecular-replacement procedure. Tens of putative models of the C-terminal domain of the protein were constructed using a multitude of homology-modelling algorithms, and these were tested for the presence of signal in molecular-replacement calculations. Of these, only the model calculated by the SAM-T08 server gave a consistent and convincing solution, but the resulting model was too inaccurate to allow phase determination to proceed to completion. The application of slow-cooling torsion-angle simulated annealing (started from a very high temperature) drastically improved this initial model to the point of allowing phasing through cycles of model building and refinement to be initiated. The structure of the protein is presented with emphasis on the presence of a C(alpha)-modified proline at its active site, which was modelled as an alpha-hydroxy-L-proline.
+
-
 
+
-
Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus.,Fadouloglou VE, Kapanidou M, Agiomirgianaki A, Arnaouteli S, Bouriotis V, Glykos NM, Kokkinidis M Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):276-83. doi:, 10.1107/S0907444912045829. Epub 2013 Jan 19. PMID:23385463<ref>PMID:23385463</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bacillus cereus atcc 14579]]
+
[[Category: Bacillus cereus ATCC 14579]]
-
[[Category: Fadouloglou, V E]]
+
[[Category: Large Structures]]
-
[[Category: Glykos, N M]]
+
[[Category: Fadouloglou VE]]
-
[[Category: Kokkinidis, M]]
+
[[Category: Glykos NM]]
-
[[Category: Hydrolase]]
+
[[Category: Kokkinidis M]]
-
[[Category: Polysaccharide deacetylase]]
+
-
[[Category: Tim barrel]]
+

Current revision

Crystal Structure of BC0361, a polysaccharide deacetylase from Bacillus cereus

PDB ID 4hd5

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4hd5"
Personal tools