6ZMY

Crystal structure of hemoglobin from turkey (Meleagiris gallopova) crystallized in monoclinic form at 1.66 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3k8b


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: https://doi.org/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 1.66 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

    Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha-A
A, C
141Meleagris gallopavoMutation(s): 0 
UniProt
Find proteins for P81023 (Meleagris gallopavo)
Explore P81023 
Go to UniProtKB:  P81023
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81023
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin beta chain
B, D
146Meleagris gallopavoMutation(s): 0 
UniProt
Find proteins for G1U9Q8 (Meleagris gallopavo)
Explore G1U9Q8 
Go to UniProtKB:  G1U9Q8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1U9Q8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.58α = 90
b = 80.52β = 96.3
c = 64.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Technology Funding CouncilUnited KingdomST/R002754/1
Foundation for Science and Technology (FCT)PortugalUIDB/04378/2020

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Derived calculations, Structure summary
  • Version 1.2: 2021-06-16
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description