9FUH | pdb_00009fuh

CRYSTAL STRUCTURE OF REDUCED WILD TYPE THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII

• PDB DOI: https://doi.org/10.2210/pdb9FUH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ralstonia pickettii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-26 Released: 2025-07-09 
• Deposition Author(s): Petchyam, N., Antonyuk, S., Hasnain, S.S.
• Funding Organization(s): UK Research and Innovation (UKRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.122 (DCC) 

Starting Model: experimental

Literature

Structural studies of haem three-domain copper nitrite reductase mutants from Ralstonia pickettii

Petchyam, N., Antonyuk, S., 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: 49.46 kDa 
• Atom Count: 4,393 
• Modeled Residue Count: 454 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	454	Ralstonia pickettii	Mutation(s): 0  Gene Names: nirK, D7S62_04310 EC: 1.7.2.1
UniProt
Find proteins for I6NAW4 (Ralstonia pickettii) Explore I6NAW4  Go to UniProtKB:  I6NAW4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	D [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4 (Subject of Investigation/LOI)	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU (Subject of Investigation/LOI)	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.122 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.842	α = 90
b = 127.842	β = 90
c = 86.337	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
Coot	model building
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Petchyam, N., Antonyuk, S., Hasnain, S.S.

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Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	BB/N013972/1
UK Research and Innovation (UKRI)	United Kingdom	BB/L006960/1

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release