PDBsum entry 1l2h

Immune system

PDB id: 1l2h

Contents

Protein chain

144 a.a. *

Waters ×126

* Residue conservation analysis

PDB id:

1l2h

Name:

Immune system

Title:

Crystal structure of interleukin 1-beta f42w/w120f mutant

Structure:

Interleukin 1-beta. Chain: a. Engineered: yes. Mutation: yes

Source:

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

Resolution:

1.54Å R-factor: 0.154 R-free: 0.193

Authors:

M.G.Rudolph,M.S.Kelker,T.R.Schneider,T.O.Yeates,V.Oseroff, D.K.Heidary,P.A.Jennings,I.A.Wilson

Key ref:

M.G.Rudolph et al. (2003). Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta. Acta Crystallogr D Biol Crystallogr, 59, 290-298. PubMed id: 12554939 DOI: 10.1107/S0907444902021704

Date:

21-Feb-02 Release date: 04-Feb-03

Protein chain

P01584  (IL1B_HUMAN) -  Interleukin-1 beta from Homo sapiens

Seq: 269 a.a.

Struc: 144 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1107/S0907444902021704

Acta Crystallogr D Biol Crystallogr 59:290-298 (2003)

PubMed id: 12554939

Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta.

M.G.Rudolph, M.S.Kelker, T.R.Schneider, T.O.Yeates, V.Oseroff, D.K.Heidary, P.A.Jennings, I.A.Wilson.

ABSTRACT

The crystal structure at 1.54 A resolution of a double mutant of interleukin-1beta (F42W/W120F), a cytokine secreted by macrophages, was determined by multiple-wavelength anomalous dispersion (MAD) using data from highly twinned selenomethionine-modified crystals. The space group is P4(3), with unit-cell parameters a = b = 53.9, c = 77.4 A. Self-rotation function analysis and various intensity statistics revealed the presence of merohedral twinning in crystals of both the native (twinning fraction alpha approximately 0.35) and SeMet (alpha approximately 0.40) forms. Structure determination and refinement are discussed with emphasis on the possible reasons for successful phasing using untreated twinned MAD data.

Selected figure(s)

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 and a Patterson integration radius of 15 Å and was contoured at <60% of the maximum peak height using POLARRFN (Collaborative Computational Project, Number 4, 1994[Collaborative Computational Program, Number 4 (1994). Acta Cryst. D50, 760-763.]). The data were reduced in P4 but the plot shows 422 symmetry, with the fourfold axis ( = 0, at the centre) and the twofold axes ( = 90°, at the perimeter) having equal heights. After detwinning of the data, the peaks for the twofold axes are absent (not shown). (b) Cumulative distribution of Z = I/, where I is the intensity, for the acentric native (black) and anomalous (blue) data. The theoretical distribution for untwinned data is shown as a dotted line. The sigmoidal shape of the distribution 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 Britton plots (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 lines).

Figure 4.
Figure 4 Ribbon representation of the final IL-1 model, with side chains drawn in ball-and-stick representation. The -strands are coloured blue, -helices red and loop regions grey. The termini are labelled. The final F[o] - F[c] simulated-annealing omit maps around the F42W and W120F mutated residues are contoured at 2.5 .

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 290-298) copyright 2003.

Figures were selected by an automated process.