View source for 3urp


==Re-refinement of PDB entry 5RNT - ribonuclease T1 with guanosine-3',5'-diphosphate and phosphate ion bound==
<StructureSection load='3urp' size='340' side='right'caption='[[3urp]], [[Resolution|resolution]] 3.19&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3urp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3URP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3URP 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]] 3.19&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGP:GUANOSINE-3,5-DIPHOSPHATE'>PGP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3urp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3urp OCA], [https://pdbe.org/3urp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3urp RCSB], [https://www.ebi.ac.uk/pdbsum/3urp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3urp ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct `target' structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 A between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.,Smart OS, Womack TO, Flensburg C, Keller P, Paciorek W, Sharff A, Vonrhein C, Bricogne G Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):368-80. Epub 2012 Mar 16. PMID:22505257<ref>PMID:22505257</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3urp" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aspergillus oryzae]]
[[Category: Large Structures]]
[[Category: Bricogne G]]
[[Category: Flensburg C]]
[[Category: Keller P]]
[[Category: Paciorek W]]
[[Category: Sharff A]]
[[Category: Smart OS]]
[[Category: Vonrhein C]]
[[Category: Womack TO]]