PDBsum entry: 9ilb

Signaling protein

PDB-id: 9ilb

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

153 a.a. *

Waters ×56

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

9ilb

Name:

Signaling protein

Title:

Human interleukin-1 beta

Structure:

Protein (human interleukin-1 beta). Chain: a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

P01584 (IL1B_HUMAN)

Seq:

269 a.a.

Struc:

153 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.28Å

R-factor:

0.157

R-free:

0.210

Authors:

B.Yu,M.Blaber,A.M.Gronenborn,G.M.Clore,D.L.D.Caspar

Key ref:

B.Yu et al. (1999). Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography.. Proc Natl Acad Sci U S A, 96, 103-108. [PubMed id: 9874779] [DOI: 10.1073/pnas.96.1.103]

Date:

22-Oct-98

Release date:

06-Jan-99

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1073/pnas.96.1.103

Proc Natl Acad Sci U S A 96:103-108 (1999)

PubMed id: 9874779

Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography.

B.Yu, M.Blaber, A.M.Gronenborn, G.M.Clore, D.L.Caspar.

ABSTRACT

Water in the hydrophobic cavity of human interleukin 1beta, which was detected by NMR spectroscopy but was invisible by high resolution x-ray crystallography, has been mapped quantitatively by measurement and phasing of all of the low resolution x-ray diffraction data from a single crystal. Phases for the low resolution data were refined by iterative density modification of an initial flat solvent model outside the envelope of the atomic model. The refinement was restrained by the condition that the map of the difference between the electron density distribution in the full unit cell and that of the atomic model be flat within the envelope of the well ordered protein structure. Care was taken to avoid overfitting the diffraction data by maintaining phases for the high resolution data from the atomic model and by a resolution-dependent damping of the structure factor differences between data and model. The cavity region in the protein could accommodate up to four water molecules. The refined solvent difference map indicates that there are about two water molecules in the cavity region. This map is compatible with an atomic model of the water distribution refined by using XPLOR. About 70% of the time, there appears to be a water dimer in the central hydrophobic cavity, which is connected to the outside by two constricted channels occupied by single water molecules approximately 40% of the time on one side and approximately 10% on the other.

Selected figure(s)

Figure 1.
Fig. 1. R factors as a function of resolution: , refined protein structure in vacuum; ×, after first cycle of difference map refinement; , after 20 cycles of refinement. Definition of R factor for the nth cycle of refinement: = \sumh||||F(h)_mod,n|| -||F(h)_obs||||||F(h)_obs|| F(h)[mod,n] is the structure factor of index hkl after the nth cycle of bulk solvent density modification, and F(h)[obs] is the observed value.

Figure 2.
Fig. 2. Difference map of the density distribution within the cavity region of the hIL-1 molecule that is not accounted for by the refined atomic model. (A) The difference electron density map within a sphere of 10-Å radius is displayed inside the C[ ]trace of an hIL-1 molecule viewed from the side containing the C terminus (center) and N terminus (top), with ball and stick representations of the cavity forming residues. The methyl groups of the aliphatic residues are drawn as large tan spheres, and the aromatic carbons are smaller, light blue spheres. Every tenth C[ ]atom is labeled, except 120, which is obscured behind the cavity density map. The red contours contain 70% of the total of 18 solvent electrons integrated in the cavity region, and the blue contours contain 50% of these electrons. (B and C) Stereopair images of the cavity solvent density within a sphere of 6-Å radius are viewed from the front (B) and back (C) of the orientation shown in A. The six leucine (L) one isoleucine (I), one valine (V), and four phenylalanine (F) residues forming the cavity are labeled. The green contours superimposed on the solvent difference map mark the envelope of the atomic model of the partially occupied water molecules in the cavity, refined with the protein model by XPLOR. This model, which contains 18.5 electrons, is contoured at the 70% level. The difference in shape of the experimental solvent difference map (red and blue) based on refinement of phases for the low resolution diffraction data and the XPLOR model of the cavity water (green) based on refinement of a single-conformer protein model may be caused by fluctuations in the cavity shape or, alternatively, to noise in diffraction data. The graphics were created with O (28), MOLSCRIPT (29), and RAYSHADE (30).