2HZV

NikR-operator DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

NikR-operator complex structure and the mechanism of repressor activation by metal ions.

Schreiter, E.R.Wang, S.C.Zamble, D.B.Drennan, C.L.

(2006) Proc Natl Acad Sci U S A 103: 13676-13681

  • DOI: 10.1073/pnas.0606247103
  • Primary Citation of Related Structures:  
    2HZA, 2HZV

  • PubMed Abstract: 
  • Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here, we report two crystal structures of nickel-activated E ...

    Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here, we report two crystal structures of nickel-activated E. coli NikR, the isolated repressor at 2.1 A resolution and in a complex with its operator DNA sequence from the nik promoter at 3.1 A resolution. Along with the previously published structure of apo-NikR, these structures allow us to evaluate functional proposals for how metal ions activate NikR, delineate the drastic conformational changes required for operator recognition, and describe the formation of a second metal-binding site in the presence of DNA. They also provide a rare set of structural views of a ligand-responsive transcription factor in the unbound, ligand-induced, and DNA-bound states, establishing a model system for the study of ligand-mediated effects on transcription factor function.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nickel-responsive regulator133Escherichia coliMutation(s): 2 
Gene Names: nikR
UniProt
Find proteins for P0A6Z6 (Escherichia coli (strain K12))
Explore P0A6Z6 
Go to UniProtKB:  P0A6Z6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6Z6
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'A [auth I],
C [auth K]
30N/A
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'B [auth J],
D [auth L]
30N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth G],
DA [auth H],
M [auth A],
Q [auth C],
T [auth D],
AA [auth G],
DA [auth H],
M [auth A],
Q [auth C],
T [auth D],
U [auth D],
V [auth E],
Y [auth F]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth G],
CA [auth G],
EA [auth H],
N [auth A],
O [auth A],
BA [auth G],
CA [auth G],
EA [auth H],
N [auth A],
O [auth A],
P [auth B],
R [auth C],
S [auth C],
W [auth E],
X [auth E],
Z [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
E [auth A],
F [auth B],
G [auth C],
H [auth D],
I [auth E],
E [auth A],
F [auth B],
G [auth C],
H [auth D],
I [auth E],
J [auth F],
K [auth G],
L [auth H]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.203α = 90
b = 76.132β = 110.27
c = 132.092γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance