1L5T

Crystal Structure of a Domain-Opened Mutant (R121D) of the Human Lactoferrin N-lobe Refined From a Merohedrally-Twinned Crystal Form.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.139 

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This is version 1.5 of the entry. See complete history


Literature

Structure of a domain-opened mutant (R121D) of the human lactoferrin N-lobe refined from a merohedrally twinned crystal form.

Jameson, G.B.Anderson, B.F.Breyer, W.A.Day, C.L.Tweedie, J.W.Baker, E.N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 955-962

  • DOI: 10.1107/s0907444902005127
  • Primary Citation of Related Structures:  
    1L5T

  • PubMed Abstract: 
  • Human lactoferrin is an iron-binding protein with a bilobal structure. Each lobe contains a high-affinity binding site for a single Fe(3+) ion and an associated CO(3)(2-) ion. Although iron binds very tightly, it can be released at low pH, with an accompanying conformational change in which the two domains move apart ...

    Human lactoferrin is an iron-binding protein with a bilobal structure. Each lobe contains a high-affinity binding site for a single Fe(3+) ion and an associated CO(3)(2-) ion. Although iron binds very tightly, it can be released at low pH, with an accompanying conformational change in which the two domains move apart. The Arg121Asp (R121D) mutant of the N-lobe half-molecule of human lactoferrin was constructed in order to test whether the Asp121 side chain could substitute for the CO(3)(2-) ion at the iron-binding site. The R121D mutant protein was crystallized in its apo form as it lost iron during crystallization. The crystals were also merohedrally twinned, with a twin fraction close to 0.5. Starting from the initial molecular-replacement solution [Breyer et al. (1999), Acta Cryst. D55, 129-138], the structure has been refined at 3.0 A resolution to an R factor of 13.9% (R(free) of 19.9%). Despite the moderate resolution, the high solvent content and non-crystallographic symmetry contributed to electron-density maps of excellent quality. Weakened iron binding by the R121D mutant is explained by occlusion of the anion-binding site by the Asp side chain. The opening of the two domains in the apoR121D structure (a rotation of 54 degrees ) closely matches that of the N-lobe in full-length lactoferrin, showing that the extent of the conformational change depends on properties inherent to the N-lobe. Differences in the C-terminal portion of the N-lobe (residues 321-332) for apoR121D relative to the closed wild-type iron-bound structure point to the importance of this region in stabilizing the open form.


    Related Citations: 
    • On the Molecular-Replacement Problem in the Presence of Merohedral Twinning: Structure of the N-Terminal Half-Molecule of Human Lactoferrin
      Breyer, W.A., Kingston, R.L., Anderson, B.F., Baker, E.N.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 129

    Organizational Affiliation

    Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
lactoferrinA, B332Homo sapiensMutation(s): 1 
Gene Names: LTFGIG12LF
EC: 1.16.1.2 (PDB Primary Data), 3.4.21 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P02788 (Homo sapiens)
Explore P02788 
Go to UniProtKB:  P02788
PHAROS:  P02788
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.139 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.3α = 90
b = 151.3β = 90
c = 48.6γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
ROTAVATAdata reduction
X-PLORmodel building
BRUTEmodel building
SHELXL-97refinement
CCP4data scaling
ROTAVATAdata scaling
X-PLORphasing
BRUTEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2021-10-27
    Changes: Database references