Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.286 
  • R-Value Observed: 0.201 

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Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change.

Jameson, G.B.Anderson, B.F.Norris, G.E.Thomas, D.H.Baker, E.N.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1319-1335

  • DOI: https://doi.org/10.1107/s0907444998004417
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The three-dimensional structure of a form of human apolactoferrin, in which one lobe (the N-lobe) has an open conformation and the other lobe (the C-lobe) is closed, has been refined at 2.0 A resolution. The refinement, by restrained least-squares methods, used synchrotron radiation X-ray diffraction data combined with a lower resolution diffractometer data set. The final refined model (5346 protein atoms from residues 1-691, two Cl- ions and 363 water molecules) gives a crystallographic R factor of 0.201 (Rfree = 0. 286) for all 51305 reflections in the resolution range 10.0-2.0 A. The conformational change in the N-lobe, which opens up the binding cleft, involves a 54 degrees rotation of the N2 domain relative to the N1 domain. This also results in a small reorientation of the two lobes relative to one another with a further approximately 730 A2 of surface area being buried as the N2 domain contacts the C-lobe and the inter-lobe helix. These new contacts also involve the C-terminal helix and provide a mechanism through which the conformational and iron-binding status of the N-lobe can be signalled to the C-lobe. Surface-area calculations indicate a fine balance between open and closed forms of lactoferrin, which both have essentially the same solvent-accessible surface. Chloride ions are bound in the anion-binding sites of both lobes, emphasizing the functional significance of these sites. The closed configuration of the C-lobe, attributed in part to weak stabilization by crystal packing interactions, has important implications for lactoferrin dynamics. It shows that a stable closed structure, essentially identical to that of the iron-bound form, can be formed in the absence of iron binding.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactotransferrin691Homo sapiensMutation(s): 0 
Gene Names: LTFGIG12LF
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P02788 (Homo sapiens)
Explore P02788 
Go to UniProtKB:  P02788
PHAROS:  P02788
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02788
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.286 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.09α = 90
b = 94.58β = 90
c = 55.79γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ALMNmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-12
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-21
    Changes: Advisory, Database references, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.5: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description