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PDBsum entry 1r3h
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Immune system
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PDB id
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1r3h
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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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Combined pseudo-Merohedral twinning, Non-Crystallographic symmetry and pseudo-Translation in a monoclinic crystal form of the gammadelta t-Cell ligand t10.
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Authors
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M.G.Rudolph,
C.Wingren,
M.P.Crowley,
Y.H.Chien,
I.A.Wilson.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2004,
60,
656-664.
[DOI no: ]
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PubMed id
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Abstract
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T10 is a non-classical class Ib-like major histocompatibility complex (MHC)
cell-surface antigen which binds directly to certain gammadelta T-cell receptors
in the absence of any exogenous and endogenous ligands, such as peculiar lipids
or glycolipids. The crystal structure at 2.5 A resolution of murine T10 was
determined by molecular replacement using data from an almost perfectly twinned
monoclinic crystal. The space group is P2(1), with unit-cell parameters a =
78.2, b = 70.0, c = 139.2 A, beta = 106.8 degrees. Self-rotation function
analysis and various intensity statistics revealed the presence of
pseudo-merohedral twinning, but these tests underestimated the true twin
fraction of alpha approximately 0.46. Native Patterson analyses pointed to the
presence of pseudo-translation among the four molecules present in the
asymmetric unit. Data analysis, structure determination and model refinement are
discussed.
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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, a Patterson integration radius of 27 Å and contoured
at >40% of the maximum peak height using POLARRFN (Collaborative
Computational Project, Number 4, 1994[Collaborative
Computational Project, Number 4 (1994). Acta Cryst. D50,
760-763.]). The data were reduced in P2, but the plot shows 222
symmetry, with one twofold axis (  =
0, at the centre) and the other twofold axes ( =
90°, at the perimeter) having equal heights. Detwinning of the
data does not change the plot owing to the presence of a
non-crystallographic twofold axis perpendicular to the b axis.
(b) Cumulative distribution of Z = I/, where I is the
intensity, for the acentric (continuous red line) and centric
(dashed red line) T10 data. The theoretical distributions for
untwinned data are shown as black lines. The sigmoidal shape of
the distribution of the acentric reflections 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
a Britton plot (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 line). The line is a
linear fit of the data with
[189]>= 0.44 and intersects the x axis at [190][alpha] = 0.37.
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Figure 4.
Figure 4 T10 structure and electron density. (a) The  [A]-weighted
3F[o] - 2F[c] electron-density map contoured at 1.5 of
the His31-Pro32 region in the  [2]m
molecule of T10 shows the presence of a cis-peptide bond which
was not modelled in the lower resolution T22 structure. (b)
Superposition of the ligand-binding site of T10 (flesh coloured)
and T22 (pale blue) shows that both MHC-like molecules are very
similar. (c) Ribbon representation of the T10 model. The -strands
in the left panel are coloured blue, -helices
red and loop regions grey. The MHC-like domains are labelled.
The loop region in T10, which replaces the first half of the
[2]-helical
segments, was not visible in the electron-density maps and is
drawn as a dashed line. The right panel shows an overlay of the
four molecules in the asymmetric unit. Each heterodimer is
individually coloured.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2004,
60,
656-664)
copyright 2004.
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