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* Residue conservation analysis
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J Mol Biol
221:239-256
(1991)
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PubMed id:
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2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten.
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A.T.Brünger,
D.J.Leahy,
T.R.Hynes,
R.O.Fox.
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ABSTRACT
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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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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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PDB code:
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Eur J Immunol,
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M.Brown,
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J Exp Med,
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PDB code:
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PDB code:
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PDB codes:
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PDB code:
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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