2ZPK

Crystal structure of P20.1 Fab fragment in complex with its antigen peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Novel affinity tag system using structurally defined antibody-tag interaction: application to single-step protein purification

Nogi, T., Sangawa, T., Tabata, S., Nagae, M., Tamura-Kawakami, K., Beppu, A., Hattori, M., Yasui, N., Takagi, J.

(2008) Protein Sci 17: 2120-2126

  • DOI: https://doi.org/10.1110/ps.038299.108
  • Primary Citation of Related Structures:  
    2ZPK

  • PubMed Abstract: 

    Biologically important human proteins often require mammalian cell expression for structural studies, presenting technical and economical problems in the production/purification processes. We introduce a novel affinity peptide tagging system that uses a low affinity anti-peptide monoclonal antibody. Concatenation of the short recognition sequence enabled the successful engineering of an 18-residue affinity tag with ideal solution binding kinetics, providing a low-cost purification means when combined with nondenaturing elution by water-miscible organic solvents. Three-dimensional information provides a firm structural basis for the antibody-peptide interaction, opening opportunities for further improvements/modifications.

    • Organizational Affiliation: 

    Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IgG1-lambda P20.1 Fab (light chain)A [auth L],
D [auth M]		212Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IgG1-lambda P20.1 Fab (heavy chain)B [auth H],
E [auth I]		216Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase-activated receptor 4C [auth P],
F [auth Q]		8N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI0 (Homo sapiens)
Explore Q96RI0 
Go to UniProtKB:  Q96RI0
PHAROS:  Q96RI0
GTEx:  ENSG00000127533 
Entity Groups  
UniProt GroupQ96RI0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA		A [auth L],
D [auth M]		L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.045α = 99.93
b = 65.271β = 93.5
c = 85.03γ = 96.46
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Derived calculations, Polymer sequence
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description