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PDBsum entry 2d98
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.8
- endo-1,4-beta-xylanase.
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Reaction:
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Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
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DOI no:
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Acta Crystallogr D Biol Crystallogr
62:280-289
(2006)
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PubMed id:
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New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL).
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H.Miyatake,
T.Hasegawa,
A.Yamano.
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ABSTRACT
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New techniques are presented for the preparation of iodine derivatives,
involving vapour diffusion of iodine. Firstly, in the vaporizing iodine
labelling (VIL) technique, a small amount of KI/I(2) solution is enclosed in a
crystallization well, with the result that gaseous I(2) molecules diffuse into
the crystallization droplets without exerting substantial changes in ionic
strength in the target crystals. Once they have diffused into the droplet, the
I(2) molecules sometimes iodinate accessible tyrosines at ortho positions.
Secondly, when iodination is insufficient, the hydrogen peroxide VIL (HYPER-VIL)
technique can be further applied to increase the iodination ratio by the
addition of a small droplet of hydrogen peroxide (H(2)O(2)) to the
crystallization well; the gaseous H(2)O(2) also diffuses into the
crystallization droplet to emphasize the iodination. These techniques are most
effective for phase determination when coupled with softer X-rays, such as those
from Cu Kalpha or Cr Kalpha radiation. The effectiveness of these techniques was
assessed using five different crystals. Four of the crystals were successfully
iodinated, providing sufficient phasing power for structure determination.
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Selected figure(s)
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Figure 3.
Figure 3 Schematic drawings of iodinated proteins prepared by
VIL and HYPER-VIL (depicted using the program NOC;
http://noc.ibp.ac.cn ; the close-up picture of Tyr95 with the
electron-density maps in VIL-thaumatin was drawn using the
program XtalView). In the molecular pictures, iodinated
tyrosines are coloured red, I atoms are in purple and tyrosines
that are not involved in iodination are drawn in cyan. (a) Left,
VIL-thaumatin with a close-up picture showing around iodinated
tyrosine Tyr95 superposed in the I-SAD phased electron-density
maps (red > 5  ,
blue > 1 );
right, HYPER-VIL-thaumatin. (b) HYPER-VIL-trypsin. (c)
HYPER-VIL-lysozyme prepared by the HYPER-VIL technique. Iodide
I2 is on a special position. (d) Left, VIL-xylanase; right,
VIL'-xylanase.
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2006,
62,
280-289)
copyright 2006.
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Figure was
selected
by an automated process.
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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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D.N.Ho,
N.C.Pomroy,
J.A.Cuesta-Seijo,
and
G.G.Privé
(2008).
Crystal structure of a self-assembling lipopeptide detergent at 1.20 A.
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Proc Natl Acad Sci U S A,
105,
12861-12866.
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PDB code:
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S.J.Wood,
X.L.Li,
M.A.Cotta,
P.Biely,
N.E.Duke,
M.Schiffer,
and
P.R.Pokkuluri
(2008).
Crystallization and preliminary X-ray diffraction analysis of the glucuronoyl esterase catalytic domain from Hypocrea jecorina.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
255-257.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
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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Links
