Loop deletion and proline insertion mutant (deleting six residues and inserted six proline residues)

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Domain-Swapping Design by Polyproline Rod Insertion.

Shiga, S.Yamanaka, M.Fujiwara, W.Hirota, S.Goda, S.Makabe, K.

(2019) Chembiochem 20: 2454-2457

  • DOI: https://doi.org/10.1002/cbic.201900179
  • Primary Citation of Related Structures:  
    6AIS, 6ICS, 6IDC, 6IEI, 6IYS

  • PubMed Abstract: 

    During domain swapping, proteins mutually interconvert structural elements to form a di-/oligomer. Engineering this process by design is important for creating a higher order protein assembly with minimal modification. Herein, a simple design strategy is shown for domain-swapping formation by loop deletion and insertion of a polyproline rod. Crystal structures revealed the formation of the domain-swapped dimers and polyproline portion formed a polyproline II (PPII) structure. Small-angle X-ray scattering demonstrated that an extended orientation of domain-swapped dimer was retained in solution. It is found that a multiple of three of inserting proline residue is favored for domain swapping because of the helical nature of PPII. The rigid nature of the polyproline rod enables precise control of the interdomain distance and orientation.

  • Organizational Affiliation

    Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata, 992-8510, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer surface protein A251Borreliella burgdorferiMutation(s): 19 
Gene Names: ospABB_A15
Find proteins for P0CL66 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31))
Explore P0CL66 
Go to UniProtKB:  P0CL66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CL66
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.383α = 90
b = 99.383β = 90
c = 102.289γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description