Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.47 kDa 
• Atom Count: 2460 
• Modelled Residue Count: 282 
• Deposited Residue Count: 282 
• Unique protein chains: 2

1CG8

CO Form Hemoglobin from Dasyatis Akajei

• PDB DOI: 10.2210/pdb1CG8/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Hemitrygon akajei
• Mutation(s): No 


• Deposited: 1999-03-26 Released: 1999-04-01 
• Deposition Author(s): Chong, K.T., Morimoto, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.252 
• R-Value Work: 0.197 

Literature

Structures of the deoxy and CO forms of haemoglobin from Dasyatis akajei, a cartilaginous fish.

Chong, K.T., Miyazaki, G., Morimoto, H., Oda, Y., Park, S.Y.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1291-1300

• PubMed: 10393295 
• DOI: 10.1107/s0907444999005934
• Primary Citation of Related Structures:  
  1CG5, 1CG8


• PubMed Abstract: 
  

The three-dimensional structures of the deoxy- and carbonmonoxyhaemoglobin (Hb) from Dasyatis akajei, a stingray, have been determined at 1.6 and 1.9 A resolution, respectively. This is one of the most distantly related vertebrate Hbs to human HbA. Both structures resemble the respective forms of HbA, indicating that the alpha2beta2-type tetramer and the mode of the quaternary structure change are common to Hbs of jawed vertebrates. Larger deviations between D. akajei Hb and human HbA are observed in various parts of the molecule, even in the E and F helices. Significant mutations and/or conformational changes are also observed around the haems, in the C-terminal region of the beta subunit, in the alpha1beta2 interface and in the organic phosphate-binding site of HbA. Despite these structural differences, the oxygen affinity, haem-haem interaction, Bohr effect and organic phosphate effect of D. akajei Hb are all only moderately reduced. Compared with human HbA, the overall r.m.s. deviation of main-chain atoms in the helical regions of bony fish Hbs is smaller than that of D. akajei Hb.

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Organizational Affiliation: 

Division of Biophysical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HEMOGLOBIN)	A	141	Hemitrygon akajei	Mutation(s): 0  Gene Names: hba
UniProt
Find proteins for P56691 (Hemitrygon akajei) Explore P56691  Go to UniProtKB:  P56691

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HEMOGLOBIN)	B	141	Hemitrygon akajei	Mutation(s): 0  Gene Names: HBB
UniProt
Find proteins for P56692 (Hemitrygon akajei) Explore P56692  Go to UniProtKB:  P56692

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.252 
• R-Value Work: 0.197 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.66	α = 90
b = 100.07	β = 90
c = 107.61	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-03-26 
• Released Date: 1999-04-01 
Deposition Author(s): Chong, K.T., Morimoto, H.

Revision History  

• Version 1.0: 1999-04-01
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance