1QJM

Crystal Structure of a Complex of Lactoferrin with a Lanthanide Ion (SM3+) at 3.4 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Lactoferrin-Metal Interactions: First Crystal Structure of a Complex of Lactoferrin with a Lanthanide Ion (Sm3+) at 3.4 Angstrom Resolution

Sharma, A.K.Singh, T.P.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1799

  • DOI: 10.1107/s0907444999009865
  • Primary Citation of Related Structures:  
    1QJM

  • PubMed Abstract: 
  • Lactoferrin is an important member of the transferrin family. A characteristic property of transferrins is their ability to bind very tightly (K(app) approximately/= 10(20)) but reversibly two Fe(3+) ions. The structural consequences of binding a metal other than Fe(3+) have been examined by crystallographic analysis at 3 ...

    Lactoferrin is an important member of the transferrin family. A characteristic property of transferrins is their ability to bind very tightly (K(app) approximately/= 10(20)) but reversibly two Fe(3+) ions. The structural consequences of binding a metal other than Fe(3+) have been examined by crystallographic analysis at 3.4 A resolution of mare samarium-lactoferrin (Sm(2)Lf). The structure was refined to an R factor of 0.219 for 8776 reflections in the resolution range 17.0-3.4 A. The samarium geometry (distorted octahedral coordination) is similar in both lobes. However, the anion interactions are quite different in the two lobes. In the N lobe, the anion is able to form only two hydrogen bonds instead of the four observed in the C lobe of Sm(2)Lf and the six observed in Fe(2)Lf. This is because Arg121, Thr117 and Gly124 have moved away from the anion as a consequence of the binding of the Sm(3+) ion. The protein ligands in the binding cleft of Sm(2)Lf show large displacements, but the overall protein structure remains the same. The binding of Sm(3+) by lactoferrin shows that the protein is capable of sequestering ions of different sizes and charges, though with reduced affinity. This conclusion should be true of other transferrins also.


    Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LACTOFERRINA689Equus caballusMutation(s): 0 
Gene Names: LTF
EC: 3.4.21
UniProt
Find proteins for O77811 (Equus caballus)
Explore O77811 
Go to UniProtKB:  O77811
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO77811
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM
Query on SM

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.492α = 90
b = 103.191β = 90
c = 113.16γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-26
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references, Derived calculations, Other, Structure summary, Version format compliance
  • Version 1.2: 2017-07-05
    Changes: Data collection
  • Version 1.3: 2019-04-03
    Changes: Data collection, Experimental preparation