1PBX

HAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII: AMINO ACID SEQUENCE, OXYGEN EQUILIBRIA AND CRYSTAL STRUCTURE OF ITS CARBONMONOXY DERIVATIVE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Haemoglobin of the antarctic fish Pagothenia bernacchii. Amino acid sequence, oxygen equilibria and crystal structure of its carbonmonoxy derivative.

Camardella, L.Caruso, C.D'Avino, R.di Prisco, G.Rutigliano, B.Tamburrini, M.Fermi, G.Perutz, M.F.

(1992) J.Mol.Biol. 224: 449-460


  • PubMed Abstract: 
  • The Antarctic fish Pagothenia bernacchii has one major haemoglobin, Hb1 (over 95% of the total blood content). Hb1 has a strong alkaline Bohr effect and at low pH exhibits the reduced ligand affinity and co-operativity that comprise the Root effect. ...

    The Antarctic fish Pagothenia bernacchii has one major haemoglobin, Hb1 (over 95% of the total blood content). Hb1 has a strong alkaline Bohr effect and at low pH exhibits the reduced ligand affinity and co-operativity that comprise the Root effect. We have determined the complete amino acid sequence of P. bernacchii Hb1 and also the structure of its carbonmonoxy derivative by X-ray crystallography, to a resolution of 2.5 A. The crystallographic R-factor of the refined structure is 18%. The three-dimensional structure of this fish haemoglobin is similar to that of human haemoglobin A, with a root-mean-square difference in main-chain atom positions of 1.4 A after superimposition of the two structures, despite only 48% homology of their amino acid sequences (including insertion of a single residue in the CD region of the fish alpha-chain). Large structural differences occur only at the N and C termini of both the alpha- and beta-chains. Neither these nor other smaller structural differences provide any obvious explanation of the Root effect of this or other fish haemoglobins.


    Organizational Affiliation

    Institute of Protein Biochemistry and Enzymology, C.N.R., Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN (CARBONMONOXY) (ALPHA CHAIN)
A
143Trematomus bernacchiiGene Names: hba
Find proteins for P80043 (Trematomus bernacchii)
Go to UniProtKB:  P80043
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN (CARBONMONOXY) (BETA CHAIN)
B
146Trematomus bernacchiiGene Names: hbb
Find proteins for P80044 (Trematomus bernacchii)
Go to UniProtKB:  P80044
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.380α = 90.00
b = 88.540β = 97.16
c = 55.340γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1991-11-04 
  • Released Date: 1992-10-15 
  • Deposition Author(s): Fermi, G.

Revision History 

  • Version 1.0: 1992-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance