1D9G

BOVINE INTERFERON-GAMMA AT 2.9 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 D Biol Crystallogr 56: 14-24

  • DOI: https://doi.org/10.1107/s0907444999014304
  • Primary Citation of Related Structures:  
    1D9C, 1D9G

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INTERFERON-GAMMA
A, B
121Bos taurusMutation(s): 0 
UniProt
Find proteins for P07353 (Bos taurus)
Explore P07353 
Go to UniProtKB:  P07353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07353
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.6α = 90
b = 79.6β = 90
c = 82.4γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-02-07
    Changes: Advisory, Data collection, Database references