5K8A

NIST FAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Data on crystal organization in the structure of the Fab fragment from the NIST reference antibody, RM 8671.

Gallagher, D.T.Karageorgos, I.Hudgens, J.W.Galvin, C.V.

(2018) Data Brief 16: 29-36

  • DOI: 10.1016/j.dib.2017.11.013
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The reported data describe the crystallization, crystal packing, structure determination and twinning of the unliganded Fab (antigen-binding fragment) from the NISTmAb (standard reference material 8671). The raw atomic coordinates are available as Pr ...

    The reported data describe the crystallization, crystal packing, structure determination and twinning of the unliganded Fab (antigen-binding fragment) from the NISTmAb (standard reference material 8671). The raw atomic coordinates are available as Protein Data Bank structure 5K8A and biological aspects are described in the article, (Karageorgos et al., 2017) [1]. Crystal data show that the packing is unique, and show the basis for the crystal's twinned growth. Twinning is a common and often serious problem in protein structure determination by x-ray crystallography [2]. In the present case the twinning is due to a small deviation (about 0.3 nm) from 4-fold symmetry in the primary intermolecular interface. The deviation produces pseudosymmetry, generating slightly different conformations of the protein, and alternating strong and weak forms of key packing interfaces throughout the lattice.


    Related Citations: 
    • Biophysical characterization and structure of the Fab fragment from the NIST reference antibody, RM 8671.
      Karageorgos, I., Gallagher, E.S., Galvin, C., Gallagher, D.T., Hudgens, J.W.
      (2017) Biologicals 50: 27

    Organizational Affiliation

    New College of Florida, Sarasota, FL 34243, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
humanized Fab Lite chainA, E, L, M213Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chainB, F, H, V227Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
B,F,H,VL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.156α = 90
b = 149.203β = 90
c = 195.032γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references