1OE1

Atomic Resolution Structure of the Wildtype Native Nitrite Reductase from Alcaligenes xylosoxidans

• PDB DOI: https://doi.org/10.2210/pdb1OE1/pdb

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


• Deposited: 2003-03-18 Released: 2003-04-17 
• Deposition Author(s): Ellis, M.J., Dodd, F.E., Hasnain, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.142 
• R-Value Observed: 0.119 

Starting Model: experimental

Literature

Atomic Resolution Structures of Native Copper Nitrite Reductase from Alcaligenes Xylosoxidans and the Active Site Mutant Asp92Glu

Ellis, M.J., Dodd, F.E., Sawers, G., Eady, R.R., Hasnain, S.S.

(2003) J Mol Biol 328: 429

• PubMed: 12691751 
• DOI: https://doi.org/10.1016/s0022-2836(03)00308-5
• Primary Citation of Related Structures:  
  1OE1, 1OE2, 1OE3


• PubMed Abstract: 
  

  We provide the first atomic resolution (<1.20 A) structure of a copper protein, nitrite reductase, and of a mutant of the catalytically important Asp92 residue (D92E). The atomic resolution where carbon-carbon bonds of the peptide become clearly resolved, remains a key goal of structural analysis. Despite much effort and technological progress, still very few structures are known at such resolution. For example, in the Protein Data Bank (PDB) there are some 200 structures of copper proteins but the highest resolution structure is that of amicyanin, a small (12 kDa) protein, which has been resolved to 1.30 A. Here, we present the structures of wild-type copper nitrite reductase (wtNiR) from Alcaligenes xylosoxidans (36.5 kDa monomer), the "half-apo" recombinant native protein and the D92E mutant at 1.04, 1.15 and 1.12A resolutions, respectively. These structures provide the basis from which to build a detailed mechanism of this important enzyme.

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Organizational Affiliation: 

Faculty of Applied Science, De Montfort University, Leicester LE1 9BH, UK.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 36.87 kDa 
• Atom Count: 3,079 
• Modelled Residue Count: 336 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE	A	336	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
CU	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.142 
• R-Value Observed: 0.119 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.725	α = 90
b = 78.725	β = 90
c = 98.885	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-17 
Deposition Author(s): Ellis, M.J., Dodd, F.E., Hasnain, S.S.

Revision History  

• Version 1.0: 2003-04-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-03-11
  Changes: Derived calculations, Polymer sequence
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary