7FAB

CRYSTAL STRUCTURE OF HUMAN IMMUNOGLOBULIN FRAGMENT FAB NEW REFINED AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human immunoglobulin fragment Fab New refined at 2.0 A resolution.

Saul, F.A.Poljak, R.J.

(1992) Proteins 14: 363-371

  • DOI: 10.1002/prot.340140305
  • Primary Citation of Related Structures:  
    7FAB

  • PubMed Abstract: 
  • The three-dimensional structure of the human immunoglobulin fragment Fab New (IgG1, lambda) has been refined to a crystallographic R-factor of 16.9% to 2 A resolution. Rms deviations of the final model from ideal geometry are 0.014 A for bond distances and 3 ...

    The three-dimensional structure of the human immunoglobulin fragment Fab New (IgG1, lambda) has been refined to a crystallographic R-factor of 16.9% to 2 A resolution. Rms deviations of the final model from ideal geometry are 0.014 A for bond distances and 3.03 degrees for bond angles. Refinement was based on a new X-ray data set including 28,301 reflections with F > 2.5 sigma(F) from 6.0 to 2.0 A resolution. The starting model for the refinement procedure reported here is from the Brookhaven Protein Data Bank entry 3FAB (rev. 1981). Differences between the initial and final models include modified polypeptide-chain folding in the third complementarity-determining region (CDR3) and the third framework region (FR3) of VH and in some exposed loops of CL and CH1. Amino acid sequence changes were determined at a number of positions by inspection of difference electron density maps. The incorporation of amino acid sequence changes results in an improved VH framework model for the "humanization" of monoclonal antibodies.


    Related Citations: 
    • Preliminary Refinement and Structural Analysis of the Fab Fragment from Human Immunoglobulin New at 2.0 Angstroms Resolution
      Saul, F.A., Amzel, L.M., Poljak, R.J.
      (1978) J Biol Chem 253: 585

    Organizational Affiliation

    Département d'Immunologie, Institut Pasteur, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG1-LAMBDA NEW FAB (LIGHT CHAIN)A [auth L]208Homo sapiensMutation(s): 0 
Gene Names: IGLC2
UniProt
Find proteins for P0DOY2 (Homo sapiens)
Explore P0DOY2 
Go to UniProtKB:  P0DOY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOY2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG1-LAMBDA NEW FAB (HEAVY CHAIN)B [auth H]217Homo sapiensMutation(s): 0 
Gene Names: IGHV4-59
UniProt
Find proteins for P01825 (Homo sapiens)
Explore P01825 
Go to UniProtKB:  P01825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01825
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.43α = 90
b = 56.68β = 116.46
c = 90.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-07-24
    Changes: Database references, Structure summary