4NC8

N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase.

Demo, G.Papouskova, V.Komarek, J.Kaderavek, P.Otrusinova, O.Srb, P.Rabatinova, A.Krasny, L.Zidek, L.Sklenar, V.Wimmerova, M.

(2014) J Struct Biol 187: 174-186

  • DOI: https://doi.org/10.1016/j.jsb.2014.06.001
  • Primary Citation of Related Structures:  
    4NC7, 4NC8

  • PubMed Abstract: 

    The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important β sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Nδ, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance.


  • Organizational Affiliation

    National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit delta
A, B
99Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpoEBSU37160
UniProt
Find proteins for P12464 (Bacillus subtilis (strain 168))
Explore P12464 
Go to UniProtKB:  P12464
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12464
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.462α = 90
b = 109.636β = 90
c = 82.928γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description