1OVB | pdb_00001ovb

THE MECHANISM OF IRON UPTAKE BY TRANSFERRINS: THE STRUCTURE OF AN 18KD NII-DOMAIN FRAGMENT AT 2.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 
    0.195 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The mechanism of iron uptake by transferrins: the structure of an 18 kDa NII-domain fragment from duck ovotransferrin at 2.3 A resolution.

Lindley, P.F.Bajaj, M.Evans, R.W.Garratt, R.C.Hasnain, S.S.Jhoti, H.Kuser, P.Neu, M.Patel, K.Sarra, R.Strange, R.Walton, A.

(1993) Acta Crystallogr D Biol Crystallogr 49: 292-304

  • DOI: https://doi.org/10.1107/S0907444992012101
  • Primary Citation Related Structures: 
    1OVB

  • PubMed Abstract: 

    The molecular structure of an iron-containing 18 kDa fragment of duck ovotransferrin, obtained by proteolysis of the intact protein, has been elucidated by protein crystallographic techniques at 2.3 A resolution. This structure supports a mechanism of iron uptake in the intact protein whereby the binding of the synergistic (bi)carbonate anion is followed by binding of the metal with the lobe in the open configuration. These stages are then followed by domain closure in which the aspartic acid residue plays a further key role, by forming an interdomain hydrogen-bond interaction in addition to serving as a ligand to the iron. This essential dual role is highlighted by model building studies on the C-terminal lobe of a known human variant. In this variant a mutation of a glycine by an arginine residue enables the aspartic acid to form an ion pair and reduce its effectiveness for both metal binding and domain closure. The X-ray structure of the 18 kDa fragment strongly suggests that the histidine residue present at the iron binding site of the intact protein and arising from the second interdomain connecting strand has been removed during the preparative proteolysis.


  • Organizational Affiliation
    • SERC Daresbury Laboratory, Warrington, Cheshire, England.

Macromolecule Content 

  • Total Structure Weight: 17.54 kDa 
  • Atom Count: 1,331 
  • Modeled Residue Count: 159 
  • Deposited Residue Count: 159 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
OVOTRANSFERRIN159Anas sp.Mutation(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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work:  0.195 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.5α = 90
b = 41.5β = 90
c = 81.9γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-10-30
    Changes: Structure summary