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PDBsum entry 1l2h
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Immune system
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PDB id
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1l2h
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta.
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Authors
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M.G.Rudolph,
M.S.Kelker,
T.R.Schneider,
T.O.Yeates,
V.Oseroff,
D.K.Heidary,
P.A.Jennings,
I.A.Wilson.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2003,
59,
290-298.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure at 1.54 A resolution of a double mutant of
interleukin-1beta (F42W/W120F), a cytokine secreted by macrophages, was
determined by multiple-wavelength anomalous dispersion (MAD) using data from
highly twinned selenomethionine-modified crystals. The space group is P4(3),
with unit-cell parameters a = b = 53.9, c = 77.4 A. Self-rotation function
analysis and various intensity statistics revealed the presence of merohedral
twinning in crystals of both the native (twinning fraction alpha approximately
0.35) and SeMet (alpha approximately 0.40) forms. Structure determination and
refinement are discussed with emphasis on the possible reasons for successful
phasing using untreated twinned MAD data.
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Figure 1.
Figure 1 Detection and analysis of twinning. (a) Stereographic
projection plot of the  =
180° section of the self-rotation function of the native data
set. The function was calculated with resolution limits of 15
and 3 Å and a Patterson integration radius of 15 Å and was
contoured at <60% of the maximum peak height using POLARRFN
(Collaborative Computational Project, Number 4,
1994[Collaborative Computational Program, Number 4 (1994). Acta
Cryst. D50, 760-763.]). The data were reduced in P4 but the plot
shows 422 symmetry, with the fourfold axis (  =
0, at the centre) and the twofold axes ( =
90°, at the perimeter) having equal heights. After detwinning of
the data, the peaks for the twofold axes are absent (not shown).
(b) Cumulative distribution of Z = I/, where I is the
intensity, for the acentric native (black) and anomalous (blue)
data. The theoretical distribution for untwinned data is shown
as a dotted line. The sigmoidal shape of the distribution
indicates potential twinning. (c) Estimation of the twin
fraction  by
plotting the cumulative fractional intensity difference of
acentric twin-related intensities, H = |I[1] - I[2]|/(I[1] +
I[2]), as a function of H (Yeates, 1988[Yeates, T. O. (1988).
Acta Cryst. A44, 142-144.]). The initial slope of the
distribution is a measure of .
The dotted lines represent the expected slopes for the indicated
twin fractions. (d) Estimation of by
Britton plots (Britton, 1972[Britton, D. (1972). Acta Cryst.
A28, 296-297.]; Fisher & Sweet, 1980[Fisher, R. G. & Sweet, R.
M. (1980). Acta Cryst. A36, 755-760.]). The number of negative
intensities after detwinning is plotted as a function of the
assumed value of .
An overestimation of will
increase the number of negative intensities and the actual value
of is
extrapolated from this increase (dotted lines).
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Figure 4.
Figure 4 Ribbon representation of the final IL-1  model,
with side chains drawn in ball-and-stick representation. The
-strands
are coloured blue, -helices
red and loop regions grey. The termini are labelled. The final
F[o] - F[c] simulated-annealing omit maps around the F42W and
W120F mutated residues are contoured at 2.5  .
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2003,
59,
290-298)
copyright 2003.
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