1CG8

CO Form Hemoglobin from Dasyatis Akajei

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

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.,Sect.D 55: 1291-1300

  • Primary Citation of Related Structures:  

  • 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. B ...

    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.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMOGLOBIN)
A
141Dasyatis akajeiMutation(s): 0 
Gene Names: hba
Find proteins for P56691 (Dasyatis akajei)
Go to UniProtKB:  P56691
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMOGLOBIN)
B
141Dasyatis akajeiMutation(s): 0 
Gene Names: HBB
Find proteins for P56692 (Dasyatis akajei)
Go to Gene View: HBB
Go to UniProtKB:  P56692
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 57.660α = 90.00
b = 100.070β = 90.00
c = 107.610γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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