1SJM

Nitrite bound copper containing nitrite reductase

• PDB DOI: https://doi.org/10.2210/pdb1SJM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Alcaligenes faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-03 Released: 2004-06-22 
• Deposition Author(s): Tocheva, E.I., Rosell, F.I., Mauk, A.G., Murphy, M.E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.138 (Depositor) 
• R-Value Work: 
  0.113 (Depositor) 
• R-Value Observed: 
  0.115 (Depositor) 

Starting Model: experimental

Literature

Side-on copper-nitrosyl coordination by nitrite reductase.

Tocheva, E.I., Rosell, F.I., Mauk, A.G., Murphy, M.E.

(2004) Science 304: 867-870

• PubMed: 15131305 
• DOI: https://doi.org/10.1126/science.1095109
• Primary Citation of Related Structures:  
  1SJM, 1SNR


• PubMed Abstract: 
  

  A copper-nitrosyl intermediate forms during the catalytic cycle of nitrite reductase, the enzyme that mediates the committed step in bacterial denitrification. The crystal structure of a type 2 copper-nitrosyl complex of nitrite reductase reveals an unprecedented side-on binding mode in which the nitrogen and oxygen atoms are nearly equidistant from the copper cofactor. Comparison of this structure with a refined nitrite-bound crystal structure explains how coordination can change between copper-oxygen and copper-nitrogen during catalysis. The side-on copper-nitrosyl in nitrite reductase expands the possibilities for nitric oxide interactions in copper proteins such as superoxide dismutase and prions.

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Organizational Affiliation: 

Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.

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)

Macromolecule Content

• Total Structure Weight: 111.57 kDa 
• Atom Count: 8,894 
• Modelled Residue Count: 1,007 
• Deposited Residue Count: 1,023 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B, C	341	Alcaligenes faecalis	Mutation(s): 0  Gene Names: NIRK, NIR EC: 1.7.2.1
UniProt
Find proteins for P38501 (Alcaligenes faecalis) Explore P38501  Go to UniProtKB:  P38501

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CU	D [auth A], E [auth A], I [auth B], J [auth B], P [auth C], Q [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT	G [auth A], L [auth B], M [auth B], N [auth B], O [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NO2	F [auth A], K [auth B], R [auth C]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.138 (Depositor) 
• R-Value Work:  0.113 (Depositor) 
• R-Value Observed: 0.115 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 102.45	β = 90
c = 145.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-22 
Deposition Author(s): Tocheva, E.I., Rosell, F.I., Mauk, A.G., Murphy, M.E.P.

Revision History  

• Version 1.0: 2004-06-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-14
  Changes: Experimental preparation
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description