6MRJ | pdb_00006mrj

Crystal structure of H.pylori NikR in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb6MRJ/pdb
• NAKB: 6MRJ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Helicobacter pylori 26695, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-13 Released: 2019-11-20 
• Deposition Author(s): Pozharski, E., de Serrano, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.241 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of H.pylori NikR in complex with DNA

Pozharski, E., de Serrano, V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 91.11 kDa 
• Atom Count: 6,025 
• Modeled Residue Count: 628 
• Deposited Residue Count: 664 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-responsive regulator	A, B, C, D	148	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: HP_1338
UniProt
Find proteins for O25896 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25896  Go to UniProtKB:  O25896

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (36-MER)	E [auth L]	36	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (36-MER)	F [auth M]	36	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI (Subject of Investigation/LOI)	G [auth A], I [auth A], J [auth B], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	H [auth A], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.241 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.37	α = 90
b = 94.18	β = 90
c = 204.06	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Pozharski, E., de Serrano, V.

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description