1LCF

CRYSTAL STRUCTURE OF COPPER-AND OXALATE-SUBSTITUTED HUMAN LACTOFERRIN AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.193 

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This is version 1.4 of the entry. See complete history


Literature

Structure of copper- and oxalate-substituted human lactoferrin at 2.0 A resolution.

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

(1994) Acta Crystallogr D Biol Crystallogr 50: 302-316

  • DOI: 10.1107/S0907444994000491
  • Primary Citation of Related Structures:  
    1LCF

  • PubMed Abstract: 
  • The three-dimensional structure of human dicupric monooxalate lactoferrin, Cu(2)oxLf, has been determined to 2.0 A resolution, using X-ray diffraction data collected by diffractometry to 2.5 A resolution, and oscillation photography on a synchrotron source to 2 ...

    The three-dimensional structure of human dicupric monooxalate lactoferrin, Cu(2)oxLf, has been determined to 2.0 A resolution, using X-ray diffraction data collected by diffractometry to 2.5 A resolution, and oscillation photography on a synchrotron source to 2.0 A resolution. Difference electron-density maps calculated between Cu(2)oxLf and both dicupric lactoferrin, Cu(2)Lf, and diferric lactoferrin, Fe(2)Lf, showed that the oxalate had replaced a carbonate in the C-terminal binding site, and that, relative to Cu(2)Lf, there were no significant differences in the N-terminal site. The structure was then refined crystallographically by restrained least-squares methods. The final model, in which the r.m.s. deviation in bond distances is 0.017 A, contains 5314 protein atoms (691 residues), two Cu(2+) ions, one bicarbonate ion, one oxalate ion, 325 solvent molecules and one sugar residue. The crystallographic R factor of 0.193 is for 46 134 reflections in the range 8.0 to 2.0 A resolution. The oxalate ion is coordinated to copper in a 1,2-bidentate fashion, and the added bulk of the anion results in the rearrangement of the side chains of nearby arginine and tyrosine residues. No other major alterations in the molecule can be observed, the overall protein structure being the same as that for Cu(2)Lf and Fe(2)Lf.


    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
    • Preliminary Crystallographic Studies of Copper(II)-and Oxalate-Substituted Human Lactoferrin
      Smith, C.A., Baker, H.M., Baker, E.N.
      (1991) J Mol Biol 219: 155
    • Structure of Human Lactoferrin: Crystallographic Structure Analysis and Refinement at 2.8 Angstroms 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LACTOFERRINA691Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
OXL
Query on OXL

Download Ideal Coordinates CCD File 
F [auth A]OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.8α = 90
b = 97.1β = 90
c = 56.2γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary