4NC7

N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.jsb.2014.06.001
  • Primary Citation of Related Structures:  

  • 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) w ...

    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

    Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic.,Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.,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.,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. Electronic address: lzidek@chemi.muni.cz.,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; Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5/A5, 62500 Brno, Czech Republic. Electronic address: michaw@chemi.muni.cz.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit delta
A, B
99Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpoE
Find proteins for P12464 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12464
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3C
Query on I3C

Download SDF File 
Download CCD File 
A
5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
5-Amino-2,4,6-triiodoisophthalic acid
C8 H4 I3 N O4
JEZJSNULLBSYHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 41.650α = 90.00
b = 110.200β = 90.00
c = 85.260γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references