3S1J

Crystal structure of acetate-bound hell's gate globin I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Hell's Gate globin I: an acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin

Teh, A.H.Saito, J.A.Baharuddin, A.Tuckerman, J.R.Newhouse, J.S.Kanbe, M.Newhouse, E.I.Rahim, R.A.Favier, F.Didierjean, C.Sousa, E.H.S.Stott, M.B.Dunfield, P.F.Gonzalez, G.Gilles-Gonzalez, M.A.Najimudin, N.Alam, M.

(2011) Febs Lett. 585: 3250-3258

  • DOI: 10.1016/j.febslet.2011.09.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hell's Gate globin I (HGbI), a heme-containing protein structurally homologous to mammalian neuroglobins, has been identified from an acidophilic and thermophilic obligate methanotroph, Methylacidiphilum infernorum. HGbI has very high affinity for O( ...

    Hell's Gate globin I (HGbI), a heme-containing protein structurally homologous to mammalian neuroglobins, has been identified from an acidophilic and thermophilic obligate methanotroph, Methylacidiphilum infernorum. HGbI has very high affinity for O(2) and shows barely detectable autoxidation in the pH range of 5.2-8.6 and temperature range of 25-50°C. Examination of the heme pocket by X-ray crystallography and molecular dynamics showed that conformational movements of Tyr29(B10) and Gln50(E7), as well as structural flexibility of the GH loop and H-helix, may play a role in modulating its ligand binding behavior. Bacterial HGbI's unique resistance to the sort of extreme acidity that would extract heme from any other hemoglobin makes it an ideal candidate for comparative structure-function studies of the expanding globin superfamily.


    Organizational Affiliation

    Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin-like flavoprotein
A, B, C
139Methylacidiphilum infernorumMutation(s): 0 
Gene Names: hmp
Find proteins for B3DUZ7 (Methylacidiphilum infernorum)
Go to UniProtKB:  B3DUZ7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 70.034α = 90.00
b = 126.225β = 90.00
c = 148.395γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
CrystalCleardata reduction
PHENIXrefinement
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2013-03-13
    Type: Database references