3AYG

Crystal structure of nitric oxide reductase complex with HQNO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LOPClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view detailsBest fitted HQOClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.

Matsumoto, Y.Tosha, T.Pisliakov, A.V.Hino, T.Sugimoto, H.Nagano, S.Sugita, Y.Shiro, Y.

(2012) Nat Struct Mol Biol 19: 238-245

  • DOI: https://doi.org/10.1038/nsmb.2213
  • Primary Citation of Related Structures:  
    3AYF, 3AYG

  • PubMed Abstract: 

    The structure of quinol-dependent nitric oxide reductase (qNOR) from G. stearothermophilus, which catalyzes the reduction of NO to produce the major ozone-depleting gas N(2)O, has been characterized at 2.5 Å resolution. The overall fold of qNOR is similar to that of cytochrome c-dependent NOR (cNOR), and some structural features that are characteristic of cNOR, such as the calcium binding site and hydrophilic cytochrome c domain, are observed in qNOR, even though it harbors no heme c. In contrast to cNOR, structure-based mutagenesis and molecular dynamics simulation studies of qNOR suggest that a water channel from the cytoplasm can serve as a proton transfer pathway for the catalytic reaction. Further structural comparison of qNOR with cNOR and aerobic and microaerobic respiratory oxidases elucidates their evolutionary relationship and possible functional conversions.


  • Organizational Affiliation

    Biometal Science Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide reductase800Geobacillus stearothermophilusMutation(s): 0 
Gene Names: norZ
Membrane Entity: Yes 
UniProt
Find proteins for B3Y963 (Geobacillus stearothermophilus)
Explore B3Y963 
Go to UniProtKB:  B3Y963
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3Y963
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LOP
Query on LOP

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BOG
Query on BOG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
HQO
Query on HQO

Download Ideal Coordinates CCD File 
K [auth A]2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
C16 H21 N O2
NZPACTGCRWDXCJ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.516α = 90
b = 149.089β = 90
c = 151.59γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LOPClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view detailsBest fitted HQOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Structure summary