1HBR

R-STATE FORM OF CHICKEN HEMOGLOBIN D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structural and functional analysis of the hemoglobin D component from chicken.

Knapp, J.E.Oliveira, M.A.Xie, Q.Ernst, S.R.Riggs, A.F.Hackert, M.L.

(1999) J Biol Chem 274: 6411-6420

  • DOI: 10.1074/jbc.274.10.6411
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Oxygen binding by chicken blood shows enhanced cooperativity at high levels of oxygen saturation. This implies that deoxy hemoglobin tetramers self-associate. The crystal structure of an R-state form of chicken hemoglobin D has been solved to 2.3-A r ...

    Oxygen binding by chicken blood shows enhanced cooperativity at high levels of oxygen saturation. This implies that deoxy hemoglobin tetramers self-associate. The crystal structure of an R-state form of chicken hemoglobin D has been solved to 2.3-A resolution using molecular replacement phases derived from human oxyhemoglobin. The model consists of an alpha2 beta2 tetramer in the asymmetric unit and has been refined to a R-factor of 0.222 (R-free = 0.257) for 29,702 reflections between 10.0- and 2.3-A resolution. Chicken Hb D differs most from human oxyhemoglobin in the AB and GH corners of the alpha subunits and the EF corner of the beta subunits. Reanalysis of published oxygen binding data for chicken Hbs shows that both chicken Hb A and Hb D possess enhanced cooperativity in vitro when inositol hexaphosphate is present. The electrostatic surface potential for a calculated model of chicken deoxy-Hb D tetramers shows a pronounced hydrophobic patch that involves parts of the D and E helices of the beta subunits. This hydrophobic patch is a promising candidate for a tetramer-tetramer interface that could regulate oxygen binding via the distal histidine.


    Related Citations: 
    • Structure of Human Oxyhaemoglobin at 2.1 A Resolution
      Shaanan, B.
      (1983) J Mol Biol 171: 31
    • The Nucleotide Sequence of the Adult Chicken Alpha-Globin Genes
      Dodgson, J.B., Engel, J.D.
      (1983) J Biol Chem 258: 4623
    • Analysis of the Adult Chicken Beta-Globin Gene
      Dolan, M., Dodgson, J.B., Engel, J.D.
      (1983) J Biol Chem 258: 3983

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMOGLOBIN D)
A, C
141Gallus gallusMutation(s): 0 
Gene Names: HBAD
Find proteins for P02001 (Gallus gallus)
Go to UniProtKB:  P02001

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMOGLOBIN D)
B, D
146Gallus gallusMutation(s): 0 
Gene Names: HBB
Find proteins for P02112 (Gallus gallus)
Go to UniProtKB:  P02112
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.96α = 90
b = 80.51β = 104.5
c = 82.11γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description