1ytt: Difference between revisions

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-[[Image:1ytt.jpg|left|200px]]
- {{Structure
+==YB SUBSTITUTED SUBTILISIN FRAGMENT OF MANNOSE BINDING PROTEIN-A (SUB-MBP-A), MAD STRUCTURE AT 110K==
-|PDB= 1ytt |SIZE=350|CAPTION= <scene name='initialview01'>1ytt</scene>, resolution 1.8&Aring;
+<StructureSection load='1ytt' size='340' side='right'caption='[[1ytt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=YB:YTTERBIUM+(III)+ION'>YB</scene>
+<table><tr><td colspan='2'>[[1ytt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YTT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YTT FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YB:YTTERBIUM+(III)+ION'>YB</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ytt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ytt OCA], [https://pdbe.org/1ytt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ytt RCSB], [https://www.ebi.ac.uk/pdbsum/1ytt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ytt ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ytt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ytt OCA], [http://www.ebi.ac.uk/pdbsum/1ytt PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ytt RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/MBL1_RAT MBL1_RAT] Calcium-dependent lectin involved in innate immune defense. Binds mannose, fucose and N-acetylglucosamine on different microorganisms and activates the lectin complement pathway. Binds to late apoptotic cells, as well as to apoptotic blebs and to necrotic cells, but not to early apoptotic cells, facilitating their uptake by macrophages (By similarity).
+== 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/yt/1ytt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ytt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A complete and accurate set of experimental crystallographic phases to a resolution of 1.8 angstroms was obtained for a 230-residue dimeric fragment of rat mannose-binding protein A with the use of multiwavelength anomalous dispersion (MAD) phasing. An accurate image of the crystal structure could thus be obtained without resort to phases calculated from a model. Partially reduced disulfide bonds, local disorder, and differences in the mobility of chemically equivalent molecules are apparent in the experimental electron density map. A solvation layer is visible that includes well-ordered sites of hydration around polar and charged protein atoms, as well as diffuse, partially disordered solvent shells around exposed hydrophobic groups. Because the experimental phases and the resulting electron density map are free from the influence of a model, they provide a stringent test of theoretical models of macromolecular solvation, motion, and conformational heterogeneity.
-'''YB SUBSTITUTED SUBTILISIN FRAGMENT OF MANNOSE BINDING PROTEIN-A (SUB-MBP-A), MAD STRUCTURE AT 110K'''
+Direct observation of protein solvation and discrete disorder with experimental crystallographic phases.,Burling FT, Weis WI, Flaherty KM, Brunger AT Science. 1996 Jan 5;271(5245):72-7. PMID:8539602<ref>PMID:8539602</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ytt" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-A complete and accurate set of experimental crystallographic phases to a resolution of 1.8 angstroms was obtained for a 230-residue dimeric fragment of rat mannose-binding protein A with the use of multiwavelength anomalous dispersion (MAD) phasing. An accurate image of the crystal structure could thus be obtained without resort to phases calculated from a model. Partially reduced disulfide bonds, local disorder, and differences in the mobility of chemically equivalent molecules are apparent in the experimental electron density map. A solvation layer is visible that includes well-ordered sites of hydration around polar and charged protein atoms, as well as diffuse, partially disordered solvent shells around exposed hydrophobic groups. Because the experimental phases and the resulting electron density map are free from the influence of a model, they provide a stringent test of theoretical models of macromolecular solvation, motion, and conformational heterogeneity.
+*[[Mannose-binding protein|Mannose-binding protein]]
+== References ==
-==About this Structure==
+<references/>
-YTT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YTT OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Direct observation of protein solvation and discrete disorder with experimental crystallographic phases., Burling FT, Weis WI, Flaherty KM, Brunger AT, Science. 1996 Jan 5;271(5245):72-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8539602 8539602]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Brunger AT]]
-[[Category: Brunger, A T.]]
+[[Category: Burling FT]]
-[[Category: Burling, F T.]]
+[[Category: Flaherty KM]]
-[[Category: Flaherty, K M.]]
+[[Category: Weis WI]]
-[[Category: Weis, W I.]]
-[[Category: calcium dependent]]
-[[Category: carbohydrate]]
-[[Category: mannose-binding protein]]
-[[Category: recognition domain]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:22:25 2008''