6ZUB | pdb_00006zub

Cu nitrite reductase from Achromobacter cycloclastes: MSOX series at 170K, dose point 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.150 (Depositor), 0.158 (DCC) 
  • R-Value Work: 
    0.124 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 
    0.126 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6ZUB

This is version 1.1 of the entry. See complete history

Literature

Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis.

Hough, M.A.Conradie, J.Strange, R.W.Antonyuk, S.V.Eady, R.R.Ghosh, A.Hasnain, S.S.

(2020) Chem Sci 11: 12485-12492

  • DOI: https://doi.org/10.1039/d0sc04797j
  • Primary Citation Related Structures: 
    6ZU6, 6ZUA, 6ZUB, 6ZUD, 6ZUT

  • PubMed Abstract: 

    The design and synthesis of copper complexes that can reduce nitrite to NO has attracted considerable interest. They have been guided by the structural information on the catalytic Cu centre of the widespread enzymes Cu nitrite reductases but the chemically novel side-on binding of NO observed in all crystallographic studies of these enzymes has been questioned in terms of its functional relevance. We show conversion of NO 2 - to NO in the crystal maintained at 170 K and present 'molecular movies' defining events during enzyme turnover including the formation of side-on Cu-NO intermediate. DFT modelling suggests that both true {CuNO} 11 and formal {CuNO} 10 states may occur as side-on forms in an enzymatic active site with the stability of the {CuNO} 10 side-on form governed by the protonation state of the histidine ligands. Formation of a copper-nitrosyl intermediate thus needs to be accommodated in future design templates for functional synthetic Cu-NiR complexes.


  • Organizational Affiliation
    • School of Life Sciences, University of Essex Wivenhoe Park Colchester CO4 3SQW UK.

Macromolecule Content 

  • Total Structure Weight: 37.13 kDa 
  • Atom Count: 3,292 
  • Modeled Residue Count: 333 
  • Deposited Residue Count: 334 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase334Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
UniProt
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25006
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLI

Query on MLI



Download:Ideal Coordinates CCD File
G [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU

Query on CU



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NO2
(Subject of Investigation/LOI)

Query on NO2



Download:Ideal Coordinates CCD File
D [auth A],
H [auth A]
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.150 (Depositor), 0.158 (DCC) 
  • R-Value Work:  0.124 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 0.126 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.356α = 90
b = 95.356β = 90
c = 95.356γ = 90
Software Package:
Software NamePurpose
SHELXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/D016290/2
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M020924/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M022714/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description