Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.13 kDa 
• Atom Count: 2360 
• Residue Count: 289 
• Unique protein chains: 2

1PBX

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

• DOI: 10.2210/pdb1PBX/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Trematomus bernacchii
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.178 

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: 1560461 
• DOI: 10.1016/0022-2836(92)91007-c
• Structures With Same Primary Citation


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HEMOGLOBIN (CARBONMONOXY) (ALPHA CHAIN)	A	143	Trematomus bernacchii	Mutation(s): 0  Gene Names: hba
Find proteins for P80043 (Pseudotrematomus bernacchii) Explore P80043  Go to UniProtKB:  P80043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HEMOGLOBIN (CARBONMONOXY) (BETA CHAIN)	B	146	Trematomus bernacchii	Mutation(s): 0  Gene Names: hbb
Find proteins for P80044 (Pseudotrematomus bernacchii) Explore P80044  Go to UniProtKB:  P80044

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	A, B	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.178 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.38	α = 90
b = 88.54	β = 97.16
c = 55.34	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance