1baf
From Proteopedia
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| - | [[Image:1baf.gif|left|200px]] | + | [[Image:1baf.gif|left|200px]] |
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| - | '''2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN''' | + | {{Structure |
| + | |PDB= 1baf |SIZE=350|CAPTION= <scene name='initialview01'>1baf</scene>, resolution 2.9Å | ||
| + | |SITE= | ||
| + | |LIGAND= <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> | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
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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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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1BAF is a [ | + | 1BAF is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BAF OCA]. |
==Reference== | ==Reference== | ||
| - | 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:// | + | 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://www.ncbi.nlm.nih.gov/pubmed/1920408 1920408] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Brunger, A T.]] | [[Category: Brunger, A T.]] | ||
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[[Category: immunoglobulin]] | [[Category: immunoglobulin]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:08:22 2008'' |
Revision as of 08:08, 20 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN
Overview
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.
About this Structure
1BAF is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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:1920408
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