2sga: Difference between revisions

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-[[Image:2sga.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2sga", creates the "Structure Box" on the page.
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-{{STRUCTURE_2sga|  PDB=2sga  |  SCENE=  }}
-'''ELECTRON DENSITY CALCULATIONS AS AN EXTENSION OF PROTEIN STRUCTURE REFINEMENT. STREPTOMYCES GRISEUS PROTEASE AT 1.5 ANGSTROMS RESOLUTION'''
+==ELECTRON DENSITY CALCULATIONS AS AN EXTENSION OF PROTEIN STRUCTURE REFINEMENT. STREPTOMYCES GRISEUS PROTEASE AT 1.5 ANGSTROMS RESOLUTION==
+<StructureSection load='2sga' size='340' side='right'caption='[[2sga]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2sga]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1sga 1sga]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2SGA 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]] 1.5&#8491;</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=2sga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2sga OCA], [https://pdbe.org/2sga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2sga RCSB], [https://www.ebi.ac.uk/pdbsum/2sga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2sga ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRTA_STRGR PRTA_STRGR] Has a primary specificity for large aliphatic or aromatic amino acids.
+== 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/sg/2sga_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=2sga ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.
-==Overview==
+Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.,Moult J, Sussman F, James MN J Mol Biol. 1985 Apr 20;182(4):555-66. PMID:3892015<ref>PMID:3892015</ref>
-Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-SGA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1sga 1sga]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SGA OCA].
+</div>
+<div class="pdbe-citations 2sga" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution., Moult J, Sussman F, James MN, J Mol Biol. 1985 Apr 20;182(4):555-66. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/3892015 3892015]
+*[[Proteinase 3D structures|Proteinase 3D structures]]
-[[Category: Single protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces griseus]]
-[[Category: James, M N.G.]]
+[[Category: James MNG]]
-[[Category: Sielecki, A R.]]
+[[Category: Sielecki AR]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 17:18:20 2008''