1OE3

Atomic resolution structure of 'Half Apo' NiR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.Biol. 328: 429

  • Primary Citation of Related Structures:  1OE1, 1OE2

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
A
336Alcaligenes xylosoxydans xylosoxydansGene Names: nir (nirK)
EC: 1.7.2.1
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  O68601
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.148 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 79.243α = 90.00
b = 79.243β = 90.00
c = 99.679γ = 120.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
DENZOdata reduction
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance