6RA6

Ferric murine neuroglobin Gly-loop44-47/F106A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report



Literature

Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy.

Milazzo, L.Exertier, C.Becucci, M.Freda, I.Montemiglio, L.C.Savino, C.Vallone, B.Smulevich, G.

(2020) FEBS J 

  • DOI: 10.1111/febs.15241
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly-loop 40-48 and G ...

    Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly-loop 40-48 and Gly-loop 44-47 ), the F106A mutant, and the double Gly-loop 44-47 /F106A mutant. Their ferric resonance Raman spectra in solution and in crystals are almost identical. In the high-frequency region, the identification of a double set of core size marker bands indicates the presence of two 6-coordinate low spin species. The resonance Raman data, together with the corresponding crystal structures, indicate the presence of two neuroglobin conformers with a reversed (A conformer) or a canonical (B conformer) heme insertion orientation. With the identification of the marker bands corresponding to each conformer, the data indicate that the B conformer increases at the expense of the A form, predominantly in the Gly-loop 44-47 /F106A double mutant, as confirmed by X-ray crystallography. This is the first time that a reversed heme insertion has been identified by resonance Raman in a native 6-coordinate low-spin heme protein. This diagnostic tool could be extended to other heme proteins in order to detect heme orientational disorder, which are likely to be correlated to functionally relevant heme dynamics. DATABASE: Crystallographic structure: structural data are deposited in the Protein Data Bank under the 6RA6 PDB entry.


    Organizational Affiliation

    Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuroglobin,Murine neuroglobin mutant,Neuroglobin
A
148Mus musculusMutation(s): 3 
Gene Names: Ngb
Find proteins for Q9ER97 (Mus musculus)
Go to UniProtKB:  Q9ER97
Small Molecules
Ligands 5 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
TRS
Query on TRS

Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.587α = 90
b = 74.587β = 90
c = 77.091γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionItaly637295

Revision History 

  • Version 1.0: 2020-03-11
    Type: Initial release