5MJD

metNgb under oxygen at 80 bar


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments.

Ardiccioni, C.Arcovito, A.Della Longa, S.van der Linden, P.Bourgeois, D.Weik, M.Montemiglio, L.C.Savino, C.Avella, G.Exertier, C.Carpentier, P.Prange, T.Brunori, M.Colloc'h, N.Vallone, B.

(2019) IUCrJ 6: 832-842

  • DOI: 10.1107/S2052252519008157
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in g ...

    A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo , solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O 2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.


    Related Citations: 
    • Neuroglobin, nitric oxide, and oxygen: functional pathways and conformational changes.
      Brunori, M., Giuffre, A., Nienhaus, K., Nienhaus, G.U., Scandurra, F.M., Vallone, B.
      (2005) Proc Natl Acad Sci U S A 102: 8483

    Organizational Affiliation

    Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences 'A. Rossi Fanelli', University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NeuroglobinA148Mus musculusMutation(s): 2 
Gene Names: Ngb
Find proteins for Q9ER97 (Mus musculus)
Explore Q9ER97 
Go to UniProtKB:  Q9ER97
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OXY
Query on OXY

Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.819α = 90
b = 87.819β = 90
c = 113.522γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references, Structure summary
  • Version 1.2: 2019-07-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.4: 2019-10-09
    Changes: Data collection, Database references