5I5M

Shewanella denitrificans nitrous oxide reductase, Ca2+-reconstituted form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase.

Schneider, L.K.Einsle, O.

(2016) Biochemistry 55: 1433-1440

  • DOI: https://doi.org/10.1021/acs.biochem.5b01278
  • Primary Citation of Related Structures:  
    5I5I, 5I5J, 5I5M

  • PubMed Abstract: 

    The copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide N₂O to dinitrogen N₂. Its maturation largely occurs in the periplasm and includes the insertion of at least one Ca²⁺ ion per monomer. Here we have investigated the role of this structural cation in recombinantly produced apo-N₂OR from Shewanella denitrificans and have determined the three-dimensional structure of the protein by X-ray crystallography. In the absence of Ca²⁺, substantial parts of the enzyme surrounding the binding sites for the copper ions show structural disorder. Reconstitution of the binuclear CuA site was possible in vitro but required the presence of Ca²⁺ ions for a stable insertion of the center. In contrast, an excess of Ca²⁺ prevented copper insertion, and the structural analysis of the Ca²⁺apo form revealed that the cation is sufficient to structure the disordered regions of the protein even in the absence of Cu ions, indicating that the geometry of the two noncanonical copper centers is largely predetermined by the protein structure.


  • Organizational Affiliation

    Institute for Biochemistry, Albert-Ludwigs-University Freiburg , 79104 Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrous-oxide reductase
A, B
638Shewanella denitrificans OS217Mutation(s): 0 
Gene Names: nosZSden_2219
EC: 1.7.2.4
UniProt
Find proteins for Q12M27 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013))
Explore Q12M27 
Go to UniProtKB:  Q12M27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12M27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BU3
Query on BU3

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B]
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.756α = 90
b = 56.978β = 105.58
c = 163.524γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany310656
German Research FoundationGermanyRTG 1976

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2016-03-23
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 2.0: 2019-10-16
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description