3FS4

Crystal structure determination of Ostrich hemoglobin at 2.2 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Literature

Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties.

Ramesh, P.Sundaresan, S.S.Shobana, N.Vinuchakkaravarthy, T.Sivakumar, K.Yasien, S.Ponnuswamy, M.N.G.

(2021) Acta Crystallogr D Struct Biol 77: 690-702

  • DOI: 10.1107/S2059798321003417
  • Primary Citation of Related Structures:  
    3FS4, 6ZMX, 6ZMY

  • PubMed Abstract: 
  • Crystal structures of hemoglobin (Hb) from two flightless birds, ostrich (Struthio camelus) and turkey (Meleagris gallopova), were determined. The ostrich Hb structure was solved to a resolution of 2.22 Å, whereas two forms of turkey Hb were solved to resolutions of 1 ...

    Crystal structures of hemoglobin (Hb) from two flightless birds, ostrich (Struthio camelus) and turkey (Meleagris gallopova), were determined. The ostrich Hb structure was solved to a resolution of 2.22 Å, whereas two forms of turkey Hb were solved to resolutions of 1.66 Å (turkey monoclinic structure; TMS) and 1.39 Å (turkey orthorhombic structure; TOS). Comparison of the amino-acid sequences of ostrich and turkey Hb with those from other avian species revealed no difference in the number of charged residues, but variations were observed in the numbers of hydrophobic and polar residues. Amino-acid-composition-based computation of various physical parameters, in particular their lower inverse transition temperatures and higher average hydrophobicities, indicated that the structures of ostrich and turkey Hb are likely to be highly ordered when compared with other avian Hbs. From the crystal structure analysis, the liganded state of ostrich Hb was confirmed by the presence of an oxygen molecule between the Fe atom and the proximal histidine residue in all four heme regions. In turkey Hb (both TMS and TOS), a water molecule was bound instead of an oxygen molecule in all four heme regions, thus confirming that they assumed the aqua-met form. Analysis of tertiary- and quaternary-structural features led to the conclusion that ostrich oxy Hb and turkey aqua-met Hb adopt the R-/R H -state conformation.


    Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit alpha-AA, C141Struthio camelusMutation(s): 0 
Gene Names: HBAA
UniProt
Find proteins for P01981 (Struthio camelus)
Explore P01981 
Go to UniProtKB:  P01981
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01981
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit betaB, D146Struthio camelusMutation(s): 0 
Gene Names: HBB
UniProt
Find proteins for P02123 (Struthio camelus)
Explore P02123 
Go to UniProtKB:  P02123
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02123
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.794α = 90
b = 81.573β = 90
c = 101.45γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-05-12
    Changes: Database references, Derived calculations
  • Version 1.3: 2021-05-19
    Changes: Database references