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CRYSTAL STRUCTURE OF HEN EGG-WHITE APO-AVIDIN IN RELATION TO ITS THERMAL STABILITY PROPERTIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of apo-avidin from hen egg-white.

Pugliese, L.Malcovati, M.Coda, A.Bolognesi, M.

(1994) J.Mol.Biol. 235: 42-46


  • PubMed Abstract: 
  • The three-dimensional structure of hen egg-white apo-avidin, crystallized in a tetragonal crystal form, has been refined to a crystallographic R-factor of 0.164 (for the 6390 observed reflections in the 10.0 to 2.8 A resolution range). As in the case ...

    The three-dimensional structure of hen egg-white apo-avidin, crystallized in a tetragonal crystal form, has been refined to a crystallographic R-factor of 0.164 (for the 6390 observed reflections in the 10.0 to 2.8 A resolution range). As in the case of holo-avidin, from which starting atomic co-ordinates were derived, the functional tetramer shows 2-pseudo 22 molecular symmetry. Each promoter is organized in an eight-stranded antiparallel orthogonal beta-barrel, with extended loop regions, which define the biotin binding pocket in the protomer core. In the absence of biotin the binding site is only partly occupied by water molecules. The structure of the binding site residues, as observed in apo-avidin, is highly complementary to that of the incoming biotin molecule, accounting for prompt and specific recognition. A crystal lattice contact may play a role in stabilizing the conformation of one protein loop, part of the biotin-binding pocket.


    Related Citations: 
    • Crystallization of Hen Egg-White Avidin in a Tetragonal Form
      Gatti, G.,Bolognesi, M.,Coda, A.,Chiolerio, F.,Filippini, E.,Malcovati, M.
      (1984) J.Mol.Biol. 178: 787
    • Three-Dimensional Structure of the Tetragonal Crystal Form of Egg-White Avidin in its Functional Complex with Biotin at 2.7 Angstroms Resolution
      Pugliese, L.,Coda, A.,Malcovati, M.,Bolognesi, M.
      (1993) J.Mol.Biol. 231: 698


    Organizational Affiliation

    Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AVIDIN
A, B
128Gallus gallusGene Names: AVD
Find proteins for P02701 (Gallus gallus)
Go to UniProtKB:  P02701
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.150α = 90.00
b = 80.150β = 90.00
c = 85.280γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance