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 2.0 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: 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 ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IgG1-lambda P20.1 Fab (light chain)A [auth L], D [auth M]212Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IgG1-lambda P20.1 Fab (heavy chain)B [auth H], E [auth I]216Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
 G [auth H], H [auth M], IGLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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

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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