Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.62 kDa 
• Atom Count: 1346 
• Modelled Residue Count: 147 
• Deposited Residue Count: 150 
• Unique protein chains: 1

1ASH

THE STRUCTURE OF ASCARIS HEMOGLOBIN DOMAIN I AT 2.2 ANGSTROMS RESOLUTION: MOLECULAR FEATURES OF OXYGEN AVIDITY

• PDB DOI: 10.2210/pdb1ASH/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Ascaris suum
• Mutation(s): No 


• Deposited: 1995-01-06 Released: 1995-02-27 
• Deposition Author(s): Yang, J., Mathews, F.S., Kloek, A.P., Goldberg, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

The structure of Ascaris hemoglobin domain I at 2.2 A resolution: molecular features of oxygen avidity.

Yang, J., Kloek, A.P., Goldberg, D.E., Mathews, F.S.

(1995) Proc Natl Acad Sci U S A 92: 4224-4228

• PubMed: 7753786 
• DOI: 10.1073/pnas.92.10.4224
• Primary Citation of Related Structures:  
  1ASH


• PubMed Abstract: 
  

The perienteric hemoglobin of the parasitic nematode Ascaris has an exceptionally high affinity for oxygen. It is an octameric protein containing two similar heme-binding domains per subunit, but recombinant constructs expressing a single, monomeric heme-binding domain (domain 1; D1) retain full oxygen avidity. We have solved the crystal structure of D1 at 2.2 A resolution. Analysis of the structure reveals a characteristic globin fold and illuminates molecular features involved in oxygen avidity of Ascaris perienteric hemoglobin. A strong hydrogen bond between tyrosine at position 10 in the B helix (tyrosine-B10) and the distal oxygen of the ligand, combined with a weak hydrogen bond between glutamine-E7 and the proximal oxygen, grips the ligand in the binding pocket. A third hydrogen bond between these two amino acids appears to stabilize the structure. The B helix of D1 is displaced laterally by 2.5 A when compared with sperm whale myoglobin. This shifts the tyrosine-B10 hydroxyl far enough from liganded oxygen to form a strong hydrogen bond without steric hindrance. Changes in the F helix compared with myoglobin contribute to a tilted heme that may also be important for oxygen affinity.

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Related Citations: 

• Expression, Characterization and Crystallization of Oxygen-Avid Ascaris Hemoglobin Domains
  Kloek, A.P., Yang, J., Mathews, F.S., Goldberg, D.E.
  (1993) J Biol Chem 268: 17669

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN (OXY)	A	150	Ascaris suum	Mutation(s): 0
UniProt
Find proteins for P28316 (Ascaris suum) Explore P28316  Go to UniProtKB:  P28316

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OXY	C [auth A]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.46	α = 90
b = 63.46	β = 90
c = 69.92	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-01-06 
• Released Date: 1995-02-27 
Deposition Author(s): Yang, J., Mathews, F.S., Kloek, A.P., Goldberg, D.E.

Revision History  

• Version 1.0: 1995-02-27
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance