1DOT

CRYSTALLOGRAPHIC STRUCTURE OF DUCK OVOTRANSFERRIN AT 2.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of diferric duck ovotransferrin at 2.35 A resolution.

Rawas, A.Muirhead, H.Williams, J.

(1996) Acta Crystallogr D Biol Crystallogr 52: 631-640

  • DOI: 10.1107/S0907444996000212
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of diferric duck ovotransferrin (DOT) has been determined and refined at a resolution of 2.35 A. The DOT structure, which contains two iron binding sites, is similar to the known transferrin and lactoferrin structures. The two iron-bind ...

    The structure of diferric duck ovotransferrin (DOT) has been determined and refined at a resolution of 2.35 A. The DOT structure, which contains two iron binding sites, is similar to the known transferrin and lactoferrin structures. The two iron-binding sites, one in the N-terminal lobe and one in the C-terminal lobe of the molecule, are similar but not identical. The main differences between the three known structures lie in the relative orientations of the N- and C-lobes with respect to each other. In the DOT structure the large aromatic side chain of Phe322 in the N-lobe packs against the conserved residue Gly387 in the C-lobe. This interaction is at the centre of the interface between the two lobes and could play a crucial role in determining their relative orientation. Other differences between the structures occur in the surface loops and in the peptide connecting the two lobes. The final crystallographic model consists of 5309 protein atoms (686 residues), two Fe(3+) ions, two (bi)carbonate ions and three carbohydrate moities. 318 water molecules have been added to the model. The final R factor is 0.22 for 25 400 observed reflections between 10 and 2.35 A resolution.


    Related Citations: 
    • Preliminary Crystallographic Studies on Duck Ovotransferrin
      Rawas, A., Moreton, K., Muirhead, H., Williams, J.
      (1989) J Mol Biol 208: 213
    • Molecular Structure of Serum Transferrin at 3.3 Angstroms Resolution
      Bailey, S., Evans, R.W., Garratt, R.C., Gorinsky, B., Hasnain, S., Horsburgh, C., Jhoti, H., Lindley, P.F., Mydin, A., Sarra, R., Watson, J.L.
      (1988) Biochemistry 27: 5804
    • Structure of Human Lactoferrin at 3.2 Angstroms Resolution
      Anderson, B.F., Baker, H.M., Dodson, E.J., Norris, G.E., Rumball, S.V., Waters, J.M., Baker, E.N.
      (1987) Proc Natl Acad Sci U S A 84: 1768

    Organizational Affiliation

    Department of Biochemistry and Molecular Recognition Centre, University of Bristol, England.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DUCK OVOTRANSFERRIN
A
686Anas platyrhynchosMutation(s): 0 
Find proteins for P56410 (Anas platyrhynchos)
Go to UniProtKB:  P56410
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
CO3
Query on CO3

Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.6α = 90
b = 85.6β = 90
c = 178.7γ = 90
Software Package:
Software NamePurpose
CCP4data collection
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
CCP4data reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Non-polymer description, Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description