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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.279 (Depositor), 0.222 (DCC)
R-Value Work:
0.229 (Depositor)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 21725560 Search on PubMed
DOI: https://doi.org/10.1039/c1dt11107h
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5Z8Y5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B]	H [auth B], J [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain H [auth B] Focus chain J [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C]	K [auth C], L [auth C], M [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain N [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain N [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], I [auth C], N [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.279 (Depositor), 0.222 (DCC)
R-Value Work: 0.229 (Depositor)
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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Benini, S.

Cianci, M.

Ciurli, S.

Revision History (Full details and data files)

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