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1baf

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[[Image:1baf.gif|left|200px]]<br /><applet load="1baf" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1baf, resolution 2.9&Aring;" />
 
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'''2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN'''<br />
 
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==Overview==
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==2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN==
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The crystal structure of the Fab fragment of the murine monoclonal anti-dinitrophenyl-spin-label antibody AN02 complexed with its hapten has been solved at 2.9 A resolution using a novel molecular replacement method. Prior to translation searches, a large number of the most likely rotation function solutions were subjected to a rigid body refinement against the linear correlation coefficient between intensities of observed and calculated structure factors. First, the overall orientation of the search model and then the orientations and positions of the four Fab domains (VH, VL, CH1 and CL) were refined. This procedure clearly identified the correct orientation of the search model. The refined search model was then subjected to translation searches which unambiguously determined the enantiomer and position in the unit cell of the crystal. The successful search model was refined 2.5 A crystal structure of the Fab fragment of HyHel-5 from which non-matching residues in the variable domains had been removed. HyHel-5 is a murine monoclonal antibody whose heavy and light chains are of the same subclass (gamma 1, kappa, respectively) as AN02. After molecular replacement the structure of the AN02 Fab has been refined using simulated annealing in combination with model building and conjugate gradient refinement to a current crystallographic R-factor of 19.5% for 12,129 unique reflections between 8.0 and 2.9 A. The root-mean-square (r.m.s.) deviation from ideal bond lengths is 0.014 A, and the r.m.s. deviation from ideal bond angles is 3.1 degrees. The electron density reveals the hapten sitting in a pocket formed by the loops of the complementarity determining region. The dinitrophenyl ring of the hapten is sandwiched between the indole rings of Trp96 of the heavy-chain and Trp91 of the light-chain. The positioning of the hapten and general features of the combining site are in good agreement with the results of earlier nuclear magnetic resonance experiments.
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<StructureSection load='1baf' size='340' side='right'caption='[[1baf]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1baf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BAF FirstGlance]. <br>
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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]] 2.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NPP:N-(2-AMINO-ETHYL)-4,6-DINITRO-N-(2,2,6,6-TETRAMETHYL-1-OXY-PIPERIDIN-4-YL)-BENZENE-1,3-DIAMINE'>NPP</scene></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=1baf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1baf OCA], [https://pdbe.org/1baf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1baf RCSB], [https://www.ebi.ac.uk/pdbsum/1baf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1baf ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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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/ba/1baf_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1baf ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1BAF is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NPP:'>NPP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BAF OCA].
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*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten., Brunger AT, Leahy DJ, Hynes TR, Fox RO, J Mol Biol. 1991 Sep 5;221(1):239-56. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1920408 1920408]
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[[Category: Large Structures]]
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[[Category: Protein complex]]
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[[Category: Mus musculus]]
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[[Category: Brunger, A T.]]
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[[Category: Brunger AT]]
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[[Category: Fox, R O.]]
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[[Category: Fox RO]]
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[[Category: Hynes, T R.]]
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[[Category: Hynes TR]]
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[[Category: Leahy, D J.]]
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[[Category: Leahy DJ]]
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[[Category: NPP]]
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[[Category: immunoglobulin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:53:13 2008''
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Current revision

2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN

PDB ID 1baf

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