1OE3 | pdb_00001oe3

Atomic resolution structure of 'Half Apo' NiR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 
    0.148 (Depositor) 
  • R-Value Observed: 
    0.116 (Depositor) 

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This is version 2.2 of the entry. See complete history. 

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 Biology 328: 429

  • DOI: https://doi.org/10.1016/s0022-2836(03)00308-5
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Faculty of Applied Science, De Montfort University, Leicester LE1 9BH, UK.

Macromolecule Content 

  • Total Structure Weight: 37.07 kDa 
  • Atom Count: 3,166 
  • Modeled Residue Count: 336 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE336Achromobacter xylosoxidansMutation(s): 0 
EC: 1.7.2.1
UniProt
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans)
Explore O68601 
Go to UniProtKB:  O68601
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68601
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free:  0.148 (Depositor) 
  • R-Value Observed: 0.116 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.243α = 90
b = 79.243β = 90
c = 99.679γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Advisory, Data collection, Derived calculations, Other, Refinement description
  • Version 2.0: 2020-03-11
    Changes: Polymer sequence
  • Version 2.1: 2025-04-09
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.2: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary