3DIF

Crystal structure of FabOX117


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A pipeline for the production of antibody fragments for structural studies using transient expression in HEK 293T cells.

Nettleship, J.E.Ren, J.Rahman, N.Berrow, N.S.Hatherley, D.Barclay, A.N.Owens, R.J.

(2008) Protein Expr Purif 62: 83-89

  • DOI: https://doi.org/10.1016/j.pep.2008.06.017
  • Primary Citation of Related Structures:  
    3DGG, 3DIF

  • PubMed Abstract: 

    We describe a pipeline for the rapid production of recombinant Fabs derived from mouse monoclonal antibodies suitable for use in structural studies. The pipeline is exemplified by the production of three Fabs derived from the monoclonal antibodies OX108 (anti-CD200 receptor), OX117 and OX119 (anti-SIRPgamma). Heavy and light chain variable domains were inserted into separate expression vectors containing resident constant regions using In-Fusion PCR cloning. Following transient co-expression in HEK 293T cells, secreted Fab fragments were purified by metal chelate chromatography and gel filtration using an automated procedure with yields of up to 4mg/L of cell culture. Following crystallization trials, diffracting crystals were obtained for the recombinant Fabs of OX108 and OX117, and their structures solved to 2.3A and 2.4A, respectively.


  • Organizational Affiliation

    The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK. ray@strubi.ox.ac.uk


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FabOX117 Light Chain Fragment
A, C
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FabOX117 Heavy Chain Fragment
B, D
229Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.206α = 101.5
b = 70.602β = 102.94
c = 87.849γ = 98.32
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-03-31
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description