4DAC

Crystal Structure of Computationally Designed Protein P6d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Computational design of a protein crystal.

Lanci, C.J.Macdermaid, C.M.Kang, S.G.Acharya, R.North, B.Yang, X.Qiu, X.J.Degrado, W.F.Saven, J.G.

(2012) Proc Natl Acad Sci U S A 109: 7304-7309

  • DOI: 10.1073/pnas.1112595109
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent int ...

    Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a "honeycomb-like" structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify "designable" structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.


    Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Computationally designed crystal forming protein P6d
A, B, C, D
28N/AMutation(s): 0 
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.669α = 90
b = 63.669β = 90
c = 40.401γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-06-13
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description