 |
PDBsum entry 2nvh
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Determination of solvent content in cavities in il-1beta using experimentally phased electron density.
|
|
|
Authors
|
|
M.L.Quillin,
P.T.Wingfield,
B.W.Matthews.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 2006,
103,
19749-19753.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The extent to which water is present within apolar cavities in proteins remains
unclear. In the case of interleukin-1beta (IL-1beta), four independent
structures solved by x-ray crystallography indicate that water is not present in
the central apolar cavity. In contrast, results from NMR spectroscopy suggest
that water has high occupancy within the cavity but is positionally disordered,
making it undetectable by standard crystallographic methods. A theoretically
based crystallographic-phase refinement technique also suggested that there was
the equivalent of two fully occupied water molecules within the apolar cavity.
To resolve these discrepancies we sought to obtain an experimentally phased
electron density map that was free of possible bias caused by mathematical
modeling of the protein or the solvent. By combining native diffraction data
with multiple wavelength anomalous data from a platinum derivative, accurate
phases were obtained. Using these experimental phases, we estimate that
occupancy of the apolar cavity in IL-1beta by solvent is close or equal to zero.
Polar cavities in the protein that contain ordered solvent molecules serve as
internal controls.
|
|
|
|
|
|
Figure 1.
Fig. 1. Electron density within cavities in IL-1  . (A)
Cavity 1. (B) Cavity 2. (C) Cavity 3. (D) Cavity 4. (E) Cavity
5. Cavity walls are rendered as translucent cyan surfaces.
Residues surrounding each cavity are displayed in ball-and-stick
format, with atoms that contact the cavity surface shown as
larger spheres. Ordered water molecules are shown as large cyan
spheres, with hydrogen-bonding interactions represented by
dotted lines. Each plot depicts experimental electron density
levels on the plane through the region of highest density (Table
4). Electron density values are represented by colors shown on
the scale, with contours every 0.5 e/Å^3 (black lines).
The cavity walls are indicated by white margins. These images
were created by using MSP (36), MOLSCRIPT (40), RASTER3D (41),
SLICED (M.L.Q., unpublished FORTRAN program), and GRI (42).
|
|
|
|
|
|
|
|
|
|
