1bww

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[[Image:1bww.gif|left|200px]]
 
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==BENCE-JONES IMMUNOGLOBULIN REI VARIABLE PORTION, T39K MUTANT==
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The line below this paragraph, containing "STRUCTURE_1bww", creates the "Structure Box" on the page.
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<StructureSection load='1bww' size='340' side='right'caption='[[1bww]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1bww]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BWW FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bww OCA], [https://pdbe.org/1bww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bww RCSB], [https://www.ebi.ac.uk/pdbsum/1bww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bww ProSAT]</span></td></tr>
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{{STRUCTURE_1bww| PDB=1bww | SCENE= }}
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</table>
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== Function ==
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'''BENCE-JONES IMMUNOGLOBULIN REI VARIABLE PORTION, T39K MUTANT'''
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[https://www.uniprot.org/uniprot/KVD33_HUMAN KVD33_HUMAN] V region of the variable domain of immunoglobulin light chains that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:20176268, PubMed:17576170).<ref>PMID:17576170</ref> <ref>PMID:20176268</ref> <ref>PMID:22158414</ref> <ref>PMID:24600447</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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==Overview==
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bw/1bww_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1bww ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
The X-ray structure of the T39K mutant of the variable domain of a human immunoglobulin kappa light chain has been determined at room temperature to 1.7 A resolution with a conventional R factor of 0. 182. T39K crystallizes in the triclinic space group P1 [a = 35.4 (1), b = 40.1 (1), c = 43.1 (1) A, alpha = 66.9 (1), beta = 85.4 (1), gamma = 73.8 (1) degrees ]. The unit-cell contains two monomers, related by a non-crystallographic twofold axis. The use of a novel type of local non-crystallographic symmetry restraints on related isotropic displacement parameters and 1-4 distances as incorporated in the refinement program SHELXL improves the model and quality of the maps, but local differences between both monomers in areas subject to different packing contacts can still be observed. 12 overall anisotropic scaling parameters were refined. These may have compensated for the difficulties in accurately scaling single rotation axis image plate data from a triclinic crystal, because of the scarcity of common equivalent reflections. The final model has been used to perform a number of tests on anisotropic scaling, non-crystallographic symmetry, anisotropic refinement, determination of standard uncertainties and bulk solvent correction. It is remarkable that removal of the NCS restraints from the final model caused Rfree to increase. These tests clarify the strategies for optimum use of SHELXL for refinement at medium as opposed to atomic resolution.
The X-ray structure of the T39K mutant of the variable domain of a human immunoglobulin kappa light chain has been determined at room temperature to 1.7 A resolution with a conventional R factor of 0. 182. T39K crystallizes in the triclinic space group P1 [a = 35.4 (1), b = 40.1 (1), c = 43.1 (1) A, alpha = 66.9 (1), beta = 85.4 (1), gamma = 73.8 (1) degrees ]. The unit-cell contains two monomers, related by a non-crystallographic twofold axis. The use of a novel type of local non-crystallographic symmetry restraints on related isotropic displacement parameters and 1-4 distances as incorporated in the refinement program SHELXL improves the model and quality of the maps, but local differences between both monomers in areas subject to different packing contacts can still be observed. 12 overall anisotropic scaling parameters were refined. These may have compensated for the difficulties in accurately scaling single rotation axis image plate data from a triclinic crystal, because of the scarcity of common equivalent reflections. The final model has been used to perform a number of tests on anisotropic scaling, non-crystallographic symmetry, anisotropic refinement, determination of standard uncertainties and bulk solvent correction. It is remarkable that removal of the NCS restraints from the final model caused Rfree to increase. These tests clarify the strategies for optimum use of SHELXL for refinement at medium as opposed to atomic resolution.
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==About this Structure==
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1.7 A structure of the stabilized REIv mutant T39K. Application of local NCS restraints.,Uson I, Pohl E, Schneider TR, Dauter Z, Schmidt A, Fritz HJ, Sheldrick GM Acta Crystallogr D Biol Crystallogr. 1999 Jun;55(Pt 6):1158-67. PMID:10329778<ref>PMID:10329778</ref>
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1BWW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BWW OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1.7 A structure of the stabilized REIv mutant T39K. Application of local NCS restraints., Uson I, Pohl E, Schneider TR, Dauter Z, Schmidt A, Fritz HJ, Sheldrick GM, Acta Crystallogr D Biol Crystallogr. 1999 Jun;55(Pt 6):1158-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10329778 10329778]
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</div>
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<div class="pdbe-citations 1bww" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Dauter, Z.]]
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[[Category: Dauter Z]]
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[[Category: Fritz, H J.]]
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[[Category: Fritz HJ]]
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[[Category: Pohl, E.]]
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[[Category: Pohl E]]
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[[Category: Schmidt, A.]]
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[[Category: Schmidt A]]
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[[Category: Schneider, T R.]]
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[[Category: Schneider TR]]
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[[Category: Sheldrick, G M.]]
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[[Category: Sheldrick GM]]
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[[Category: Uson, I.]]
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[[Category: Uson I]]
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[[Category: Bence-jones protein]]
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[[Category: Reiv]]
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[[Category: Stabilized immunoglobulin fragment]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 12:03:19 2008''
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Current revision

BENCE-JONES IMMUNOGLOBULIN REI VARIABLE PORTION, T39K MUTANT

PDB ID 1bww

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