1DZB

Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Phage Library-Derived Single-Chain Fv Fragment Complexed with Turkey Egg -White Lysozyme at 2.0 A Resolution

Ay, J.Keitel, T.Kuttner, G.Wessner, H.Scholz, C.Hahn, M.Hohne, W.

(2000) J.Mol.Biol. 301: 239

  • DOI: 10.1006/jmbi.2000.3971

  • PubMed Abstract: 
  • The three-dimensional structure of the single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme (TEL) has been determined to a nominal resolution of 2.0 A by X-ray diffraction. The scFv fragment 1F9 was derived from phage-display librar ...

    The three-dimensional structure of the single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme (TEL) has been determined to a nominal resolution of 2.0 A by X-ray diffraction. The scFv fragment 1F9 was derived from phage-display libraries in two steps and binds both hen and turkey egg-white lysozyme, although the level of binding affinity is two orders of magnitude greater for the turkey lysozyme. The comparison of the crystal structure with a model of the single-chain Fv fragment 1F9 in complex with hen egg-white lysozyme (HEL) reveals that in the latter a clash between Asp101 in lysozyme and Trp98 of the complementarity determining region H3 of the heavy chain variable domain occurs. This is the only explanation apparent from the crystal structure for the better binding of TEL compared to HEL. The binding site topology on the paratope is not simply a planar surface as is usually found in antibody-protein interfaces, but includes a cleft between the light chain variable domain and heavy chain variable domain large enough to accommodate a loop from the lysozyme. The scFv fragment 1F9 recognizes an epitope on TEL that differs from the three antigenic determinants recognized in other known crystal structures of monoclonal antibodies in complex with lysozyme.


    Related Citations: 
    • A Phage Library-Derived Single-Chain Fv Fragment in Complex with a Phage Library-Derived Single-Chain Fv Fragment in Complex Withturkey Egg-White Lysozyme: Characterization, Crystallization Andpreliminary X-Ray Analysis
      Kuttner, G.,Keitel, T.,Giessmann, E.,Wessner, H.,Scholz, C.
      (1998) Mol.Immunol. 35: 189


    Organizational Affiliation

    Abteilung Proteinstrukturforschung, Institut für Biochemie des Universitätsklinikums Charité der Humboldt-Universität zu Berlin, Monbijoustr. 2, Berlin, 10117, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SCFV FRAGMENT 1F9
A, B
253N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TURKEY EGG-WHITE LYSOZYME C
X, Y
129Meleagris gallopavoGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00703 (Meleagris gallopavo)
Go to Gene View: LYZ
Go to UniProtKB:  P00703
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.710α = 90.00
b = 112.440β = 97.67
c = 80.000γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-02
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance