5X3F

Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.

Youn, S.J.Kwon, N.Y.Lee, J.H.Kim, J.H.Choi, J.Lee, H.Lee, J.O.

(2017) Sci Rep 7: 2595-2595

  • DOI: 10.1038/s41598-017-02803-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Generating artificial protein assemblies with complex shapes requires a method for connecting protein components with stable and predictable structures. Currently available methods for creating rigid protein assemblies rely on either complicated calc ...

    Generating artificial protein assemblies with complex shapes requires a method for connecting protein components with stable and predictable structures. Currently available methods for creating rigid protein assemblies rely on either complicated calculations or extensive trial and error. We describe a simple and efficient method for connecting two proteins via a fused alpha helix that is formed by joining two preexisting helices into a single extended helix. Because the end-to-end ligation of helices does not guarantee the formation of a continuous helix, we superimposed 1-2 turns of pairs of connecting helices by using a molecular graphics program. Then, we chose amino acids from the two natural sequences that would stabilize the connecting helix. This "shared helix method" is highly efficient. All the designed proteins that could be produced in Escherichia coli were readily crystallized and had the expected fusion structures. To prove the usefulness of this method, we produced two novel repeat proteins by assembling several copies of natural or artificial proteins with alpha helices at both termini. Their crystal structures demonstrated the successful assembly of the repeating units with the intended curved shapes. We propose that this method could dramatically expand the available repertoire of natural repeat proteins.


    Organizational Affiliation

    Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea.,Institute of Biotechnology, Chungnam National University, Daejeon, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea. jieoh@kaist.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putrescine aminotransferase,Immunoglobulin G-binding protein A
A
501Escherichia coli (strain K12)Staphylococcus aureus
This entity is chimeric
Mutation(s): 2 
Gene Names: patA (ygjG), spa
EC: 2.6.1.82
Find proteins for P42588 (Escherichia coli (strain K12))
Go to UniProtKB:  P42588
Find proteins for P38507 (Staphylococcus aureus)
Go to UniProtKB:  P38507
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Zpa963,cAMP-dependent protein kinase catalytic subunit alpha
B
393Mus musculusMutation(s): 0 
Gene Names: Prkaca (Pkaca)
EC: 2.7.11.11
Find proteins for P05132 (Mus musculus)
Go to UniProtKB:  P05132
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.190 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 140.518α = 90.00
b = 153.496β = 90.00
c = 205.714γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release