Experimental Data Snapshot

  • Resolution: 2.76 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable.

Ratnaparkhi, G.S.Ramachandran, S.Udgaonkar, J.B.Varadarajan, R.

(1998) Biochemistry 37: 6958-6966

  • DOI: https://doi.org/10.1021/bi972857n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the C82A mutant of barstar, the intracellular inhibitor of the Bacillus amyloliquefaciens ribonuclease barnase, has been solved to a resolution of 2.8 A. The molecule crystallizes in the space group I41 with a dimer in the asymmetric unit. An identical barstar dimer is also found in the crystal structure of the barnase-barstar complex. This structure of uncomplexed barstar is compared to the structure of barstar bound to barnase and also to the structure of barstar solved using NMR. The free structure is similar to the bound state, and there are no significant main-chain differences in the 27-44 region involved in barstar binding to barnase. The C82A structure shows significant differences from the average NMR structure, both overall and in the binding region. In contrast to the crystal structure, the NMR structure shows an unusually high packing value based on the occluded surface algorithm, indicating errors in the packing of the structure. We show that the NMR structures of homologous proteins generally show large differences in packing value, while the crystal structures of such proteins have very similar packing values, suggesting that protein packing density is not well determined by NMR.

  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
90Bacillus amyloliquefaciensMutation(s): 1 
Find proteins for P11540 (Bacillus amyloliquefaciens)
Explore P11540 
Go to UniProtKB:  P11540
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11540
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.76 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.182α = 90
b = 104.182β = 90
c = 36γ = 90
Software Package:
Software NamePurpose
MARXDSdata reduction
MARSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references
  • Version 1.4: 2023-08-02
    Changes: Refinement description