6RKZ | pdb_00006rkz

Recombinant Pseudomonas stutzeri nitrous oxide reductase, form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.191 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.152 (Depositor) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6RKZ

This is version 1.2 of the entry. See complete history

Literature

Functional assembly of nitrous oxide reductase provides insights into copper site maturation.

Zhang, L.Wust, A.Prasser, B.Muller, C.Einsle, O.

(2019) Proc Natl Acad Sci U S A 116: 12822-12827

  • DOI: https://doi.org/10.1073/pnas.1903819116
  • Primary Citation Related Structures: 
    6RKZ, 6RL0

  • PubMed Abstract: 

    The multicopper enzyme nitrous oxide reductase reduces the greenhouse gas N 2 O to uncritical N 2 as the final step of bacterial denitrification. Its two metal centers require an elaborate assembly machinery that so far has precluded heterologous production as a prerequisite for bioremediatory applications in agriculture and wastewater treatment. Here, we report on the production of active holoenzyme in Escherichia coli using a two-plasmid system to produce the entire biosynthetic machinery as well as the structural gene for the enzyme. Using this recombinant system to probe the role of individual maturation factors, we find that the ABC transporter NosFY and the accessory NosD protein are essential for the formation of the [4Cu:2S] site Cu Z , but not the electron transfer site Cu A Depending on source organism, the heterologous host E. coli can, in some cases, compensate for the lack of the Cu chaperone NosL, while in others this protein is strictly required, underlining the case for designing a recombinant system to be entirely self-contained.


  • Organizational Affiliation
    • Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 146.03 kDa 
  • Atom Count: 10,253 
  • Modeled Residue Count: 1,172 
  • Deposited Residue Count: 1,292 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrous-oxide reductase
A, B
646Stutzerimonas stutzeriMutation(s): 0 
Gene Names: nosZ
EC: 1.7.2.4
UniProt
Find proteins for P19573 (Stutzerimonas stutzeri)
Explore P19573 
Go to UniProtKB:  P19573
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19573
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CUZ
(Subject of Investigation/LOI)

Query on CUZ



Download:Ideal Coordinates CCD File
O [auth A],
Y [auth B]
(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
Cu4 S
IGIWMDIIFLPFOP-UHFFFAOYSA-N
B3P

Query on B3P



Download:Ideal Coordinates CCD File
C [auth A],
Q [auth B]
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
CUA

Query on CUA



Download:Ideal Coordinates CCD File
P [auth A],
Z [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
U [auth B],
V [auth B],
W [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
S [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
F [auth A],
T [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
D [auth A],
R [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.191 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.152 (Depositor) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.887α = 90
b = 76.789β = 93.33
c = 108.823γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany310656

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description