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PDBsum entry 1c1m
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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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Exploring hydrophobic sites in proteins with xenon or krypton.
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Authors
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T.Prangé,
M.Schiltz,
L.Pernot,
N.Colloc'H,
S.Longhi,
W.Bourguet,
R.Fourme.
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Ref.
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Proteins, 1998,
30,
61-73.
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PubMed id
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Abstract
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X-ray diffraction is used to study the binding of xenon and krypton to a variety
of crystallised proteins: porcine pancreatic elastase; subtilisin Carlsberg from
Bacillus licheniformis; cutinase from Fusarium solani; collagenase from
Hypoderma lineatum; hen egg lysozyme, the lipoamide dehydrogenase domain from
the outer membrane protein P64k from Neisseria meningitidis; urate-oxidase from
Aspergillus flavus, mosquitocidal delta-endotoxin CytB from Bacillus
thuringiensis and the ligand-binding domain of the human nuclear retinoid-X
receptor RXR-alpha. Under gas pressures ranging from 8 to 20 bar, xenon is able
to bind to discrete sites in hydrophobic cavities, ligand and substrate binding
pockets, and into the pore of channel-like structures. These xenon complexes can
be used to map hydrophobic sites in proteins, or as heavy-atom derivatives in
the isomorphous replacement method of structure determination.
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Secondary reference #1
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Title
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Protein crystallography at ultra-Short wavelengths: feasability study of anomalous-Dispersion experiments at the xenon k-Edge
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Authors
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M.Schiltz,
A.Kvick,
O.Svensson,
W.Shepard,
E.De la fortelle,
T.Prange,
R.Kahn.
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Ref.
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j synchrotron radia, 1997,
4,
287.
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Secondary reference #2
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Title
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High-Pressure krypton gas and statistical heavy-Atom refinement: a successful combination of tools for macromolecular structure determination.
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Authors
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M.Schiltz,
W.Shepard,
R.Fourme,
T.Prangé,
E.De la fortelle,
G.Bricogne.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1997,
53,
78-92.
[DOI no: ]
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PubMed id
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Figure 3.
Fig. 3. Isotherrns (293 K) of xenon and krypton binding to PPE. The
quantity
p/k,
which is equivalent to the occupancy of the heavy
atom, is plotted
versus
the gas pressure P. p is the nlaximum density
(corresponding to the bound heavy atom) in a difference-Fourier
,nap and k is a normalization factor that was obtained for each
curve by least-squares fitting of the experimental data points
(p,P)
to the function,
p/k
= AP/(I + AP) The lined curves are shown as
dashed lines.
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Figure 4.
Fig. 4. Fluorescence spectrum of krypton gas.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #3
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Title
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The catalytic site of serine proteinases as a specific binding cavity for xenon.
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Authors
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M.Schiltz,
R.Fourme,
I.Broutin,
T.Prangé.
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Ref.
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Structure, 1995,
3,
309-316.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Close-up stereoview of the active site region of PPE.
The refined structure of the xenon complex is superposed on a
2.2 å resolution (F[Xe]-F[nat]) difference-Fourier map.
The map is contoured at the 10σ (blue) and at the 20σ (red)
levels (where σ is the rms of the whole map density). The
single spherical peak (with maximum density of 31σ) corresponds
to a xenon atom bound into the active site. Also displayed
(pink) are the side chains of the residues belonging to the
catalytic triad. Figure 4. Close-up stereoview of the active
site region of PPE. The refined structure of the xenon complex
is superposed on a 2.2 å resolution (F[Xe]-F[nat])
difference-Fourier map. The map is contoured at the 10σ (blue)
and at the 20σ (red) levels (where σ is the rms of the whole
map density). The single spherical peak (with maximum density of
31σ) corresponds to a xenon atom bound into the active site.
Also displayed (pink) are the side chains of the residues
belonging to the catalytic triad.
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Figure 6.
Figure 6. Close-up view of the active site region of subtilisin
Carlsberg from B. licheniformis. The Cα backbone chain (green)
of the native structure is superposed on a 2.2 å
resolution (F[Xe]-F[nat]) difference-Fourier map. The map is
contoured at the 8σ (blue) and at the 14σ (pink) levels
(where σ is the rms of the whole map density). The single
spherical peak (with maximum density of 21σ) corresponds to a
xenon atom bound into the active site. Also displayed are the
side chains of the residues belonging to the catalytic triad.
Figure 6. Close-up view of the active site region of subtilisin
Carlsberg from B. licheniformis. The Cα backbone chain (green)
of the native structure is superposed on a 2.2 å
resolution (F[Xe]-F[nat]) difference-Fourier map. The map is
contoured at the 8σ (blue) and at the 14σ (pink) levels (where
σ is the rms of the whole map density). The single spherical
peak (with maximum density of 21σ) corresponds to a xenon atom
bound into the active site. Also displayed are the side chains
of the residues belonging to the catalytic triad.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #4
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Title
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On the preparation and X-Ray data collection of isomorphous xenon derivatives
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Authors
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M.Schiltz,
T.Prange,
R.Fourme.
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Ref.
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j appl crystallogr, 1994,
27,
950.
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