1OE2

Atomic Resolution Structure of D92E Mutant of Alcaligenes xylosoxidans Nitrite Reductase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.179 
  • R-Value Observed: 0.163 

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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

  • DOI: 10.1016/s0022-2836(03)00308-5
  • Primary Citation of Related Structures:  
    1OE3, 1OE2, 1OE1

  • 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 reso ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASEA336Achromobacter xylosoxidansMutation(s): 1 
Gene Names: nir, nirK, ERS451415_02178
EC: 1.7.2.1
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans)
Explore O68601 
Go to UniProtKB:  O68601
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4
Download Ideal Coordinates CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
CU
Query on CU
Download Ideal Coordinates CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA		AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.179 
  • R-Value Observed: 0.163 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.7α = 90
b = 78.7β = 90
c = 98.9γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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 1.3: 2019-05-22
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 2.0: 2020-03-11
    Changes: Polymer sequence