PDBsum entry 1d9c

Immune system

PDB id: 1d9c

Contents

Protein chains

121 a.a. *

Waters ×130

* Residue conservation analysis

PDB id:

1d9c

Name:

Immune system

Title:

Bovine interferon-gamma at 2.0 angstroms

Structure:

Interferon-gamma. Chain: a, b. Engineered: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.201 R-free: 0.275

Authors:

M.Randal,A.A.Kossiakoff

Key ref:

M.Randal and A.A.Kossiakoff (2000). The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species. Acta Crystallogr D Biol Crystallogr, 56, 14-24. PubMed id: 10666622 DOI: 10.1107/S0907444999014304

Date:

27-Oct-99 Release date: 10-Nov-99

Protein chains

P07353  (IFNG_BOVIN) -  Interferon gamma from Bos taurus

Seq: 166 a.a.

Struc: 121 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1107/S0907444999014304

Acta Crystallogr D Biol Crystallogr 56:14-24 (2000)

PubMed id: 10666622

The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species.

M.Randal, A.A.Kossiakoff.

ABSTRACT

The structure of bovine interferon-gamma (IFN-gamma) was determined by multiple isomorphous replacement at 2.0 A resolution. Bovine IFN-gamma crystallizes in two related crystal forms. Crystal form 1 diffracts to 2.9 A resolution and is reproducible and stable to derivatization. Crystal form 2 diffracts to 2.0 A resolution, but shows significant non-isomorphism from crystal to crystal. The previously determined structures of several different species of INF-gamma were either at too low a resolution [human, 1hig; Ealick et al. (1991), Science, 252, or were too inaccurate [bovine, 1rfb; Samudzi & Rubin (1993), Acta Cryst. D49(6), 505-512; rabbit, 2rig; Samudzi et al. (1991), J. Biol. Chem. for the structure to be solved by molecular replacement. The structure was solved in crystal form 1 using two derivatives produced by chemically modifying two free cysteine residues that were introduced by site-directed mutagenesis (Ser30Cys, Asn59Cys). After model building and refinement, the final R value was 21.8% (R(free) = 30.9%) for all data in the resolution range 8.0-2.9 A. The crystal form 1 structure was then used as a molecular-replacement model for crystal form 2 data collected from a flash-cooled crystal. Subsequent model building and refinement, using all data in the resolution range 15.0-2.0 A, gave an R value of 19.7% and an R(free) of 27.5%. Pairwise comparison of C(alpha) positions of bovine IFN-gamma (BOV) and the previously determined 1rfb and 2rig structures indicated some significant differences in the models (r.m.s.d. values for BOV to 1rfb, 4.3 A; BOV to 2rig, 4.0 A). An assessment of the quality of the structures was made using the 3D-1D algorithm [Eisenberg et al. (1992), Faraday Discuss. 93, 25-34]. The resulting statistical scoring indicated that BOV was consistent with expected criteria for a 2.0 A structure, whereas both 1rfb and 2rig fell below acceptable criteria.

Selected figure(s)

Figure 2.
Figure 2 Stereoview of a portion of the electron-density map superimposed on residues 36-55 for (a) the NCS-averaged solvent-flattened MIR map, (b) the crystal form 1 2F[o] - F[c] map (1 , 2.9 Å) and (c) the crystal form 2 2F[o] - F[c] map (1 , 2.0 Å).

Figure 9.
Figure 9 (a) van der Waals surface representation of the residues lining the buried cavity in bovine IFN- . (b) Substitution of a low-energy conformation of Trp at residue 33 results in the elimination of this cavity.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 14-24) copyright 2000.

Figures were selected by an automated process.