1D9G

BOVINE INTERFERON-GAMMA AT 2.9 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

Randal, M.Kossiakoff, A.A.

(2000) Acta Crystallogr.,Sect.D 56: 14-24

  • Primary Citation of Related Structures:  1D9C

  • PubMed 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 ...

    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, 698-702] or were too inaccurate [bovine, 1rfb; Samudzi & Rubin (1993), Acta Cryst. D49(6), 505-512; rabbit, 2rig; Samudzi et al. (1991), J. Biol. Chem. 266(32), 21791-21797] 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.


    Organizational Affiliation

    Graduate Group in Biophysics, University of California, San Francisco, California 94000, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTERFERON-GAMMA
A, B
121Bos taurusGene Names: IFNG
Find proteins for P07353 (Bos taurus)
Go to Gene View: IFNG
Go to UniProtKB:  P07353
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.600α = 90.00
b = 79.600β = 90.00
c = 82.400γ = 90.00
Software Package:
Software NamePurpose
AUTOMARdata reduction
XDSdata reduction
PHASESphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description