2Y3Y

Holo-Ni(II) HpNikR is a symmetric tetramer containing four canonic square-planar Ni(II) ions at physiological pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Holo-Ni(2+)Helicobacter Pylori Nikr Contains Four Square-Planar Nickel-Binding Sites at Physiological Ph.

Benini, S.Cianci, M.Ciurli, S.

(2011) Dalton Trans 40: 7831

  • DOI: 10.1039/c1dt11107h

  • PubMed Abstract: 
  • The crystal structure of Helicobacter pylori holo-NikR, a Ni(2+)-dependent transcription factor, determined at pH 7.3, shows four square-planar nickel-binding sites, involving one cysteinate and three histidine ligands. This observation reconciles pr ...

    The crystal structure of Helicobacter pylori holo-NikR, a Ni(2+)-dependent transcription factor, determined at pH 7.3, shows four square-planar nickel-binding sites, involving one cysteinate and three histidine ligands. This observation reconciles previous inconsistencies among calorimetric data, structural information at non-physiological pH, and computational studies.


    Organizational Affiliation

    Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy. stefano.benini@unibz.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE NICKEL-RESPONSIVE REGULATOR
A, B, C, D
91Helicobacter pylori (strain G27)Mutation(s): 0 
Find proteins for B5Z8Y5 (Helicobacter pylori (strain G27))
Go to UniProtKB:  B5Z8Y5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UNDECAPEPTIDE-GSSSGSASGAG
Q
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
B, C
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 72.970α = 90.00
b = 72.970β = 90.00
c = 116.730γ = 90.00
Software Package:
Software NamePurpose
HKL2MAPphasing
REFMACrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release