1OXY

CRYSTALLOGRAPHIC ANALYSIS OF OXYGENATED AND DEOXYGENATED STATES OF ARTHROPOD HEMOCYANIN SHOWS UNUSUAL DIFFERENCES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences.

Magnus, K.A.Hazes, B.Ton-That, H.Bonaventura, C.Bonaventura, J.Hol, W.G.

(1994) Proteins 19: 302-309

  • DOI: 10.1002/prot.340190405

  • PubMed Abstract: 
  • The X-ray structure of an oxygenated hemocyanin molecule, subunit II of Limulus polyphemus hemocyanin, was determined at 2.4 A resolution and refined to a crystallographic R-factor of 17.1%. The 73-kDa subunit crystallizes with the symmetry of the sp ...

    The X-ray structure of an oxygenated hemocyanin molecule, subunit II of Limulus polyphemus hemocyanin, was determined at 2.4 A resolution and refined to a crystallographic R-factor of 17.1%. The 73-kDa subunit crystallizes with the symmetry of the space group R32 with one subunit per asymmetric unit forming hexamers with 32 point group symmetry. Molecular oxygen is bound to a dinuclear copper center in the protein's second domain, symmetrically between and equidistant from the two copper atoms. The copper-copper distance in oxygenated Limulus hemocyanin is 3.6 +/- 0.2 A, which is surprisingly 1 A less than that seen previously in deoxygenated Limulus polyphemus subunit II hemocyanin (Hazes et al., Protein Sci. 2:597, 1993). Away from the oxygen binding sites, the tertiary and quaternary structures of oxygenated and deoxygenated Limulus subunit II hemocyanins are quite similar. A major difference in tertiary structures is seen, however, when the Limulus structures are compared with deoxygenated Panulirus interruptus hemocyanin (Volbeda, A., Hol, W.G.J.J. Mol. Biol. 209:249, 1989) where the position of domain 1 is rotated by 8 degrees with respect to domains 2 and 3. We postulate this rotation plays an important role in cooperativity and regulation of oxygen affinity in all arthropod hemocyanins.


    Related Citations: 
    • Hexamers of Subunit II from Limulus Hemocyanin (A 48mer) Have the Same Quaternary Structure as Whole Panulirus Hemocyanin Molecules
      Magnus, K.A.,Lattman, E.E.,Volbeda, A.,Hol, W.G.L.
      (1991) Proteins 9: 240
    • Crystals of a Functional 70,000 Molecular Weight Subunit of Hemocyanin from Limulus Polyphemus
      Magnus, K.A.,Love, W.E.
      (1977) J.Mol.Biol. 116: 171


    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106-4935.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOCYANIN (SUBUNIT TYPE II)
A
628Limulus polyphemusN/A
Find proteins for P04253 (Limulus polyphemus)
Go to UniProtKB:  P04253
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.171 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 117.240α = 90.00
b = 117.240β = 90.00
c = 285.860γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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