6F1Q | pdb_00006f1q

Crystal structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii in I213 space group

• PDB DOI: https://doi.org/10.2210/pdb6F1Q/pdb

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


• Deposited: 2017-11-22 Released: 2018-06-27 
• Deposition Author(s): Antonyuk, S., Sasaki, D., Eady, R.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: 2.30 Å
• R-Value Free: 
  0.162 (Depositor), 0.166 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Substrate entry and binding requires activation of tyrosine in heme-copper nitrite reductase

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: 50.69 kDa 
• Atom Count: 3,977 
• Modeled Residue Count: 456 
• 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	D [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
CU	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.162 (Depositor), 0.166 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.853	α = 90
b = 180.853	β = 90
c = 180.853	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Antonyuk, S., Sasaki, D., Eady, R.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 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary