6FJA | pdb_00006fja

Crystal structure of T2D three-domain heme-Cu nitrite reductase from Ralstonia pickettii

• PDB DOI: https://doi.org/10.2210/pdb6FJA/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Ralstonia pickettii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-21 Released: 2018-06-27 
• Deposition Author(s): Antonyuk, S.V., Eady, R., Hasnain, S.S.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.175 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Activation of redox tyrosine switch is required for ligand binding at the catalytic site in heme-cu nitrite reductases

Dong, J., Sasaki, D., Eady, R., Antonyuk, S.V., Hasnain, S.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.63 kDa 
• Atom Count: 3,908 
• Modeled Residue Count: 455 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite reductase	A	468	Ralstonia pickettii	Mutation(s): 0  EC: 1.7.2.1
UniProt
Find proteins for I6NAW4 (Ralstonia pickettii) Explore I6NAW4  Go to UniProtKB:  I6NAW4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.175 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.23	α = 90
b = 128.23	β = 90
c = 86.11	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Antonyuk, S.V., Eady, R., Hasnain, S.S.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/L006960/1

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 2.0: 2024-01-17
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary