1BKA

OXALATE-SUBSTITUTED DIFERRIC LACTOFERRIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Anion binding by transferrins: importance of second-shell effects revealed by the crystal structure of oxalate-substituted diferric lactoferrin.

Baker, H.M.Anderson, B.F.Brodie, A.M.Shongwe, M.S.Smith, C.A.Baker, E.N.

(1996) Biochemistry 35: 9007-9013

  • DOI: 10.1021/bi960288y

  • PubMed Abstract: 
  • Proteins of the transferrin family bind, with high affinity, two Fe3+ ions and two CO3(2)- ions but can also bind other metal ions and other anions. In order to find out how the protein structure and its two binding sites adapt to the binding of larg ...

    Proteins of the transferrin family bind, with high affinity, two Fe3+ ions and two CO3(2)- ions but can also bind other metal ions and other anions. In order to find out how the protein structure and its two binding sites adapt to the binding of larger anions, we have determined the crystal structure of oxalate-substituted diferric lactoferrin at 2.4 A resolution. The final model has a crystallographic R-factor of 0.196 for all data in the range 8.0-2.4 A. Substitution of oxalate for carbonate does not produce any significant change in the polypeptide folding or domain closure. Both binding sites are perturbed, however, and the effects are different in each. In the C-lobe site the oxalate ion is bound to iron in symmetric 1,2-bidentate fashion whereas in the N-lobe the anion coordination is markedly asymmetric. The difference arises because in each site substitution of the larger anion causes displacement of the arginine that forms one wall of the anion binding site; the movement is different in each case, however, because of different interactions with "second shell" amino acid residues in the binding cleft. These observations provide an explanation for the site inequivalences that accompany the substitution of non-native anions and cations.


    Related Citations: 
    • Anion Binding by Human Lactoferrin: Results from Crystallographic and Physicochemical Studies
      Shongwe, M.S.,Smith, C.A.,Ainscough, E.W.,Baker, H.M.,Brodie, A.M.,Baker, E.N.
      (1992) Biochemistry 31: 4451
    • Structure of Human Diferric Lactoferrin Refined at 2.2 Angstroms Resolution
      Haridas, M.,Anderson, B.F.,Baker, E.N.
      (1995) Acta Crystallogr.,Sect.D 51: 629
    • Structure of Human Lactoferrin: Crystallographic Structure Analysis and Refinement at 2.8 A Resolution
      Anderson, B.F.,Baker, H.M.,Norris, G.E.,Rice, D.W.,Baker, E.N.
      (1989) J.Mol.Biol. 209: 711


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand. T.Baker@massey.ac.nz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LACTOFERRIN
A
691Homo sapiensMutation(s): 0 
Gene Names: LTF (GIG12, LF)
EC: 3.4.21.-
Find proteins for P02788 (Homo sapiens)
Go to Gene View: LTF
Go to UniProtKB:  P02788
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXL
Query on OXL

Download SDF File 
Download CCD File 
A
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 155.460α = 90.00
b = 96.920β = 90.00
c = 55.850γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
WEISdata collection
WEISdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance