4KYZ

Three-dimensional structure of triclinic form of de novo design insertion domain, Northeast Structural Genomics Consortium (NESG) Target OR327


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.492 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Precise assembly of complex beta sheet topologies from de novo designed building blocks.

King, I.C.Gleixner, J.Doyle, L.Kuzin, A.Hunt, J.F.Xiao, R.Montelione, G.T.Stoddard, B.L.DiMaio, F.Baker, D.

(2015) Elife 4: --

  • DOI: 10.7554/eLife.11012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Design of complex alpha-beta protein topologies poses a challenge because of the large number of alternative packing arrangements. A similar challenge presumably limited the emergence of large and complex protein topologies in evolution. Here, we dem ...

    Design of complex alpha-beta protein topologies poses a challenge because of the large number of alternative packing arrangements. A similar challenge presumably limited the emergence of large and complex protein topologies in evolution. Here, we demonstrate that protein topologies with six and seven-stranded beta sheets can be designed by insertion of one de novo designed beta sheet containing protein into another such that the two beta sheets are merged to form a single extended sheet, followed by amino acid sequence optimization at the newly formed strand-strand, strand-helix, and helix-helix interfaces. Crystal structures of two such designs closely match the computational design models. Searches for similar structures in the SCOP protein domain database yield only weak matches with different beta sheet connectivities. A similar beta sheet fusion mechanism may have contributed to the emergence of complex beta sheets during natural protein evolution.


    Organizational Affiliation

    Institute for Protein Design, University of Washington, Seattle, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Designed protein OR327
A, B, C, D
172N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.492 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.819α = 82.03
b = 55.402β = 80.34
c = 78.258γ = 90.03
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2015-12-23
    Type: Database references
  • Version 1.2: 2016-01-13
    Type: Database references
  • Version 1.3: 2016-02-17
    Type: Database references