1BQ5

NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051

• PDB DOI: https://doi.org/10.2210/pdb1BQ5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Achromobacter xylosoxidans
• Mutation(s): No 


• Deposited: 1998-08-21 Released: 1999-08-21 
• Deposition Author(s): Inoue, T., Gotowda, M., Deligeer, Suzuki, S., Kataoka, K., Yamaguchi, K., Watanabe, H., Goho, M., Yasushi, K.A.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 

Literature

Type 1 Cu structure of blue nitrite reductase from Alcaligenes xylosoxidans GIFU 1051 at 2.05 A resolution: comparison of blue and green nitrite reductases.

Inoue, T., Gotowda, M., Deligeer, Kataoka, K., Yamaguchi, K., Suzuki, S., Watanabe, H., Gohow, M., Kai, Y.

(1998) J Biochem 124: 876-879

• PubMed: 9792907 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a022201
• Primary Citation of Related Structures:  
  1BQ5


• PubMed Abstract: 
  

  The crystal structure of the blue nitrite reductase from Alcaligenes xylosoxidans GIFU 1051 (AxgNIR) has been determined at 2.05 A resolution. AxgNIR contains both type 1 and 2 Cu sites, the geometry of the former being distorted tetrahedral. The superpositioning of the type 1 Cu sites in the blue enzyme and a green nitrite reductase revealed that the orientation of the Met150 side chain differed. The deviation of the Sdelta(Met150) atom from the axial position of the NNS plane formed by two Ndelta(His95 and His145) and one Sgamma(Cys136) atom caused the difference in the colors of the enzymes, i.e. blue and green.

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Organizational Affiliation: 

Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 37.26 kDa 
• Atom Count: 2,657 
• Modelled Residue Count: 333 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITRITE REDUCTASE	A	342	Achromobacter xylosoxidans	Mutation(s): 0  EC: 1.7.2.1
UniProt
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans) Explore O68601  Go to UniProtKB:  O68601

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.565	α = 90
b = 106.565	β = 90
c = 63.578	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-21 
Deposition Author(s): Inoue, T., Gotowda, M., Deligeer, Suzuki, S., Kataoka, K., Yamaguchi, K., Watanabe, H., Goho, M., Yasushi, K.A.I.

Revision History  

• Version 1.0: 1999-08-21
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations