1GV8

18 kDa fragment of N-II domain of duck ovotransferrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Mechanism of Iron Uptake by Transferrins: The X-Ray Structures of the 18 kDa Nii Domain Fragment of Duck Ovotransferrin and its Nitrilotriacetate Complex

Kuser, P.Hall, D.R.Haw, M.L.Neu, M.Evans, R.Lindley, P.F.

(2002) Acta Crystallogr D Biol Crystallogr 58: 777

  • DOI: 10.1107/s0907444902003724
  • Primary Citation of Related Structures:  
    1GV8, 1GVC

  • PubMed Abstract: 
  • In a previous paper [Lindley et al. (1993), Acta Cryst. D49, 292-304], the X-ray structure analysis of the 18 kDa fragment of duck ovotransferrin, corresponding to the NII domain of the intact protein, was reported at a resolution of 2.3 A. In this structure, the Fe(III) cation binds to two tyrosine residues and the synergistic carbonate anion in an identical manner to that found in the intact protein ...

    In a previous paper [Lindley et al. (1993), Acta Cryst. D49, 292-304], the X-ray structure analysis of the 18 kDa fragment of duck ovotransferrin, corresponding to the NII domain of the intact protein, was reported at a resolution of 2.3 A. In this structure, the Fe(III) cation binds to two tyrosine residues and the synergistic carbonate anion in an identical manner to that found in the intact protein. However, the aspartate and histidine residues, normally involved in iron binding in transferrins, are absent in the fragment and it was not possible to unequivocally define what had replaced them. The electron density was tentatively assigned to be a mixture of peptides, presumably resulting from the proteolytic preparation of the fragment, binding to the iron through their amino and carboxylate termini. A more recent X-ray analysis of the fragment, from a different preparation, has resulted in a structure at 1.95 A, in which glycine appears to be the predominant residue bound to the cation. In an alternative attempt to clarify the binding of iron to the 18 kDa fragment, the metal was removed by dialysis and replaced in the form of ferric nitrilotriacetate. Crystallization of this complex has resulted in an X-ray structure at 1.90 A in which the Fe(III) is bound to the synergistic carbonate anion and only one tyrosine residue in a manner almost identical to the intact protein. The carboxylate groups and the tertiary amino group of the nitrilotriacetate occupy the remaining coordination sites. The second tyrosine residue, Tyr95, is not bound directly to the iron. The implication of these structures with respect to the mechanism of iron binding by the transferrins is addressed.


    Organizational Affiliation

    Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OVOTRANSFERRINA159Anas platyrhynchosMutation(s): 0 
UniProt
Find proteins for P56410 (Anas platyrhynchos)
Explore P56410 
Go to UniProtKB:  P56410
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56410
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download Ideal Coordinates CCD File 
B [auth A]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
C [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
D [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.39α = 90
b = 41.39β = 90
c = 81.57γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Agrovatadata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation