2rns: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2rns.png|left|200px]]
-<!--
+==REFINEMENT OF THE CRYSTAL STRUCTURE OF RIBONUCLEASE S. COMPARISON WITH AND BETWEEN THE VARIOUS RIBONUCLEASE A STRUCTURES==
-The line below this paragraph, containing "STRUCTURE_2rns", creates the "Structure Box" on the page.
+<StructureSection load='2rns' size='340' side='right'caption='[[2rns]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2rns]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovin Bovin]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rns 1rns]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RNS FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
--->
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>
-{{STRUCTURE_2rns|  PDB=2rns  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rns OCA], [https://pdbe.org/2rns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rns RCSB], [https://www.ebi.ac.uk/pdbsum/2rns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rns ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rn/2rns_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rns ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribonuclease S (RNase-S) is a complex that consists of two proteolytic fragments of bovine pancreatic ribonuclease A (RNase-A): the S-peptide (residues 1-20) and S-protein (residues 21-124). We have refined the crystal structures of three RNase-S complexes. The first two contain the full-length 20-residue S-peptide and were studied at pHs of 4.75 and 5.5. The third one consists of a truncated form of S-peptide (residues 1-15) and was studied at pH 4.75 as the reference structure for a series of mutant peptide complexes to be reported separately. Excluding residues 16-23 which are either missing (in the S15 complex) or disordered (in both S20 complexes), all three structures refined at 1.6-A resolution are identical within the estimated errors in the coordinates (0.048 A for the backbone atoms). The R-values, residual error, range from 17.4% to 18.6%. The final model of S20, pH 4.75, includes 1 sulfate and 84 water molecules. The side chains of 11 residues were modeled in two discrete conformations. The final structures were independent of the particular RNase-A or RNase-S used as a starting model. An extensive comparison with refined crystal structures of RNase-A reveals that the core of the molecule which is held together with extensive hydrogen bonds is in identical pattern in all cases. However, the loop regions vary from one structure to another and are often characterized by high B-factors. The pattern of thermal parameters appears to be dependent on crystal packing and correlates well with the accessibility calculated in the crystal. Gln60 is a conserved residue in all sequences known to date for this class of ribonucleases. However, it is the only residue that is clearly defined in an unfavorable position (phi = -100 degrees, psi = -130 degrees) on the Ramachandran plot. The origin of the substantial differences between RNase-A and RNase-S in stability to both acid and temperature denaturation and in susceptibility to proteolysis at neutral pH is not obvious in our visual comparison of these two structures.
-===REFINEMENT OF THE CRYSTAL STRUCTURE OF RIBONUCLEASE S. COMPARISON WITH AND BETWEEN THE VARIOUS RIBONUCLEASE A STRUCTURES===
+Refinement of the crystal structure of ribonuclease S. Comparison with and between the various ribonuclease A structures.,Kim EE, Varadarajan R, Wyckoff HW, Richards FM Biochemistry. 1992 Dec 15;31(49):12304-14. PMID:1463719<ref>PMID:1463719</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2rns" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_1463719}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 1463719 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_1463719}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bovin]]
-RNS is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rns 1rns]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNS OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:1463719</ref><references group="xtra"/>
-[[Category: Bos taurus]]
 [[Category: Pancreatic ribonuclease]]
-[[Category: Kim, E E.]]
+[[Category: Kim, E E]]
-[[Category: Richards, F M.]]
+[[Category: Richards, F M]]
-[[Category: Varadarajan, R.]]
+[[Category: Varadarajan, R]]
-[[Category: Wyckoff, H W.]]
+[[Category: Wyckoff, H W]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:21:59 2009''