1AIV

APO OVOTRANSFERRIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of hen apo-ovotransferrin. Both lobes adopt an open conformation upon loss of iron

Kurokawa, H.Dewan, J.C.Mikami, B.Sacchettini, J.C.Hirose, M.

(1999) J.Biol.Chem. 274: 28445-28452


  • PubMed Abstract: 
  • The three-dimensional crystal structure of hen apo-ovotransferrin has been solved by molecular replacement and refined by simulated annealing and restrained least squares to a 3.0-A resolution. The final model, which comprises 5312 protein atoms (res ...

    The three-dimensional crystal structure of hen apo-ovotransferrin has been solved by molecular replacement and refined by simulated annealing and restrained least squares to a 3.0-A resolution. The final model, which comprises 5312 protein atoms (residues 1 to 686) and 28 carbohydrate atoms (from two monosaccharides attached to Asn(473)), gives an R-factor of 0.231 for the 11,989 observed reflections between 20.0- and 3.0-A resolution. In the structure, both empty iron binding clefts are in the open conformation, lending weight to the theory that Fe(3+) binding or release in transferrin proceeds via a mechanism that involves domain opening and closure. Upon opening, the domains rotate essentially as rigid bodies. The two domains of the N-lobe rotate away from one another by 53 degrees, whereas the C-lobe domains rotate away each another by 35 degrees. These rotations take place about an axis that passes through the two beta-strands, linking the domains. The domains of each lobe make different contacts with one another in the open and closed forms. These contacts form two interdomain interfaces on either side of the rotation axis, and domain opening or closing produces a see-saw motion between these two alternative close-packed interfaces. The interdomain disulfide bridge (Cys(478)-Cys(671)), found only in the C-lobe, may restrict domain opening but does not completely prevent it.


    Related Citations: 
    • Crystal Structure of Diferric Hen Ovotransferrin at 2.4 A Resolution
      Kurokawa, H.,Mikami, B.,Hirose, M.
      (1995) J.Mol.Biol. 254: 196


    Organizational Affiliation

    Research Institute for Food Science, Kyoto University, Uji, Kyoto 611, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OVOTRANSFERRIN
A
686Gallus gallusN/A
Find proteins for P02789 (Gallus gallus)
Go to UniProtKB:  P02789
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.260α = 90.00
b = 92.260β = 90.00
c = 178.190γ = 90.00
Software Package:
Software NamePurpose
SAINTdata scaling
X-PLORmodel building
X-PLORphasing
SAINTdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance