5K8A image
Deposition Date 2016-05-27
Release Date 2017-08-09
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5K8A
Keywords:
Title:
NIST FAB
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.18
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Heavy chain
Chain IDs:B (auth: H), D (auth: V), F (auth: B), H (auth: F)
Chain Length:227
Number of Molecules:4
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:humanized Fab Lite chain
Chain IDs:A (auth: L), C (auth: M), E (auth: A), G (auth: E)
Chain Length:213
Number of Molecules:4
Biological Source:Mus musculus
Primary Citation
Data on crystal organization in the structure of the Fab fragment from the NIST reference antibody, RM 8671.
Data Brief 16 29 36 (2018)
PMID: 29167817 DOI: 10.1016/j.dib.2017.11.013

Abstact

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.

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