2Y3Y | pdb_00002y3y

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

• PDB DOI: https://doi.org/10.2210/pdb2Y3Y/pdb

• Classification: TRANSCRIPTION
• Organism(s): Helicobacter pylori G27, unidentified
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-04 Released: 2011-08-17 
• Deposition Author(s): Benini, S., Cianci, M., Ciurli, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

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

• PubMed: 21725560 
• DOI: https://doi.org/10.1039/c1dt11107h
• Primary Citation of Related Structures:  
  2Y3Y


• 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 previous inconsistencies among calorimetric data, structural information at non-physiological pH, and computational studies.

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Organizational Affiliation: 

Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.57 kDa 
• Atom Count: 2,807 
• Modelled Residue Count: 341 
• Deposited Residue Count: 375 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE NICKEL-RESPONSIVE REGULATOR	A, B, C, D	91	Helicobacter pylori G27	Mutation(s): 0
UniProt
Find proteins for B5Z8Y5 (Helicobacter pylori (strain G27)) Explore B5Z8Y5  Go to UniProtKB:  B5Z8Y5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UNDECAPEPTIDE-GSSSGSASGAG	E [auth Q]	11	unidentified	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	H [auth B], J [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG	K [auth C], L [auth C], M [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NI	F [auth A], G [auth B], I [auth C], N [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.97	α = 90
b = 72.97	β = 90
c = 116.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Benini, S., Cianci, M., Ciurli, S.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other