Biological Assembly 1  

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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: 60475.22 
• Atom Count: 3626 
• Residue Count: 532 
• Unique protein chains: 1

1Q5V

Apo-NikR

• DOI: 10.2210/pdb1Q5V/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• 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: 2.3 Å
• R-Value Free: 0.305 
• R-Value Work: 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.Mol.Biol. 10: 794-799

• PubMed: 12970756 
• DOI: 10.1038/nsb985
• Primary Citation of Related Structures:  
  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

Find similar proteins by: Sequence  |  Structure

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.305 
• R-Value Work: 0.248 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 46.360	α = 90.00
b = 69.530	β = 90.00
c = 158.810	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	refinement
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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance