Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.84 kDa 
• Atom Count: 1482 
• Modelled Residue Count: 152 
• Deposited Residue Count: 152 
• Unique protein chains: 1

1X3K

Crystal structure of a hemoglobin component (TA-V) from Tokunagayusurika akamusi

• PDB DOI: 10.2210/pdb1X3K/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Tokunagayusurika akamusi
• Mutation(s): No 


• Deposited: 2005-05-09 Released: 2005-05-24 
• Deposition Author(s): Kuwada, T., Hasegawa, T., Sato, S., Sato, I., Ishikawa, K., Takagi, T., Shishikura, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 

Literature

Crystal structures of two hemoglobin components from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera).

Kuwada, T., Hasegawa, T., Sato, S., Sato, I., Ishikawa, K., Takagi, T., Shishikura, F.

(2007) Gene 398: 29-34

• PubMed: 17590288 
• DOI: 10.1016/j.gene.2007.02.049
• Primary Citation of Related Structures:  
  1X3K, 1X46


• PubMed Abstract: 
  

The polymorphic components of hemoglobin (Hb) of the midge larva Propsilocerus akamusi were classified into two distinct types dependent on their spectroscopic properties, normal absorption (N) and low absorption (L). Analyses of the amino acid sequences of component VII (N-type Hb) and component V (L-type Hb) from P. akamusi indicated that one remarkable difference is the replacement of the distal histidine (His) with isoleucine (Ile) in component V. To clarify the structural differences between the two Hb components, we determined the crystal structures of components V and VII at resolutions of 1.64 A and 1.50 A, respectively. These crystal structures indicated a short additional helix comprising three amino acid residues at the C-terminal region in component V, and a typical globin fold including eight helices in component VII. Comparison of the heme regions of the Hb components suggests that the structural changes of the heme region in component V on ligation differ from that of usual Hb.

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Organizational Affiliation: 

Advanced Research Institute for the Sciences and Humanities, Nihon University, Chiyoda-ku, Tokyo 102-8251, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemoglobin component V	A	152	Tokunagayusurika akamusi	Mutation(s): 0
UniProt
Find proteins for Q7M422 (Tokunagayusurika akamusi) Explore Q7M422  Go to UniProtKB:  Q7M422

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.144	α = 90
b = 74.855	β = 90
c = 33.412	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-09 
• Released Date: 2005-05-24 
Deposition Author(s): Kuwada, T., Hasegawa, T., Sato, S., Sato, I., Ishikawa, K., Takagi, T., Shishikura, F.

Revision History  

• Version 1.0: 2005-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance