3S1J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.febslet.2011.09.002
  • Primary Citation of Related Structures:  
    3S1I, 3S1J

  • 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(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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin-like flavoprotein
A, B, C
139Methylacidiphilum infernorum V4Mutation(s): 0 
Gene Names: hmpMinf_1095
UniProt
Find proteins for B3DUZ7 (Methylacidiphilum infernorum (isolate V4))
Explore B3DUZ7 
Go to UniProtKB:  B3DUZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3DUZ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
J [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
L [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
K [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.034α = 90
b = 126.225β = 90
c = 148.395γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations