5N8I

Serial Cu nitrite reductase structures at elevated cryogenic temperature, 100K reference dataset.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.

Sen, K.Horrell, S.Kekilli, D.Yong, C.W.Keal, T.W.Atakisi, H.Moreau, D.W.Thorne, R.E.Hough, M.A.Strange, R.W.

(2017) IUCrJ 4: 495-505

  • DOI: 10.1107/S2052252517007527
  • Primary Citation of Related Structures:  
    5N8H, 5N8G, 5N8I, 5N8F

  • PubMed Abstract: 
  • Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulation ...

    Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (Asp CAT and His CAT ) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the Asp CAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (Ile CAT ), a determinant of ligand binding, are influenced both by temperature and by the protonation state of Asp CAT . A previously unobserved conformation of Ile CAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.


    Organizational Affiliation

    School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseA334Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.793α = 90
b = 94.793β = 90
c = 94.793γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M020924/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M022714/1

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references