Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.48 kDa 
• Atom Count: 3648 
• Modelled Residue Count: 476 
• Deposited Residue Count: 532 
• Unique protein chains: 1

1Q5V

Apo-NikR

• PDB DOI: 10.2210/pdb1Q5V/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-08-11 Released: 2003-09-30 
• Deposition Author(s): Schreiter, E.R., Sintchak, M.D., Guo, Y., Chivers, P.T., Sauer, R.T., Drennan, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.305 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 

Literature

Crystal Structure of the Nickel-Responsive Transcription Factor NikR

Schreiter, E.R., Sintchak, M.D., Guo, Y., Chivers, P.T., Sauer, R.T., Drennan, C.L.

(2003) Nat Struct Biol 10: 794-799

• PubMed: 12970756 
• DOI: 10.1038/nsb985
• Primary Citation of Related Structures:  
  1Q5V, 1Q5Y


• PubMed Abstract: 
  

NikR is a metal-responsive transcription factor that controls nickel uptake in Escherichia coli by regulating expression of a nickel-specific ATP-binding cassette (ABC) transporter. We have determined the first two structures of NikR: the full-length apo repressor at a resolution of 2.3 A and the nickel-bound C-terminal regulatory domain at a resolution of 1.4 A. NikR is the only known metal-responsive member of the ribbon-helix-helix family of transcription factors, and its structure has a quaternary arrangement consisting of two dimeric DNA-binding domains separated by a tetrameric regulatory domain that binds nickel. The position of the C-terminal regulatory domain enforces a large spacing between the contacts that each NikR DNA-binding domain can make with the nik operator. The regulatory domain of NikR contains four nickel-binding sites at the tetramer interface, each exhibiting a novel square-planar coordination by three histidines and one cysteine side chain.

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Organizational Affiliation: 

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel responsive regulator	A, B, C, D	133	Escherichia coli	Mutation(s): 0  Gene Names: nikR
UniProt
Find proteins for P0A6Z6 (Escherichia coli (strain K12)) Explore P0A6Z6  Go to UniProtKB:  P0A6Z6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.305 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.36	α = 90
b = 69.53	β = 90
c = 158.81	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-11 
• Released Date: 2003-09-30 
Deposition Author(s): Schreiter, E.R., Sintchak, M.D., Guo, Y., Chivers, P.T., Sauer, R.T., Drennan, C.L.

Revision History  

• Version 1.0: 2003-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance