1HBI

CRYSTAL STRUCTURE OF OXYGENATED SCAPHARCA DIMERIC HEMOGLOBIN AT 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of oxygenated Scapharca dimeric hemoglobin at 1.7-A resolution.

Condon, P.J.Royer Jr., W.E.

(1994) J Biol Chem 269: 25259-25267

  • DOI: 10.2210/pdb1hbi/pdb
  • Primary Citation of Related Structures:  
    1HBI

  • PubMed Abstract: 
  • The crystal structure of the cooperative dimeric hemoglobin from the blood clam Scapharca inaequivalvis has been determined in the oxygenated state and refined to an R-factor of 0.157 at 1.7-A resolution. The structure is very similar to the carbon monoxide-liganded form with subtle differences in ligand binding geometry ...

    The crystal structure of the cooperative dimeric hemoglobin from the blood clam Scapharca inaequivalvis has been determined in the oxygenated state and refined to an R-factor of 0.157 at 1.7-A resolution. The structure is very similar to the carbon monoxide-liganded form with subtle differences in ligand binding geometry. Oxygen binds to the heme iron in a bent conformation with Fe-O-O angles of 135 degrees and 150 degrees for the two subunits. These observed angles are lower than the equivalent angles in the carbon monoxide-liganded form and intermediate between the angles observed in structures of oxygenated sperm whale myoglobin and oxygenated human hemoglobin. This third high resolution structure of Scapharca dimeric hemoglobin permits a detailed analysis of the water structure in the highly hydrated interface between subunits.


    Related Citations: 
    • High-Resolution Crystallographic Analysis of a Co-Operative Dimeric Hemoglobin
      Royer Junior, W.E.
      (1994) J Mol Biol 235: 657
    • Structural Transitions Upon Ligand Binding in a Cooperative Dimeric Hemoglobin
      Royer Junior, W.E., Hendrickson, W.A., Chiancone, E.
      (1990) Science 249: 518

    Organizational Affiliation

    Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester 01605.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEMOGLOBIN (OXY) AB146Anadara inaequivalvisMutation(s): 0 
Find proteins for P02213 (Anadara inaequivalvis)
Explore P02213 
Go to UniProtKB:  P02213
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
OXY
Query on OXY

Download Ideal Coordinates CCD File 
A, B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.2α = 90
b = 44β = 122
c = 83.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance