3T43

Crystal Structure of HIV Epitope-Scaffold 4E10_1XIZA_S0_006_C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-resolution structure prediction of a circular permutation loop.

Correia, B.E.Holmes, M.A.Huang, P.S.Strong, R.K.Schief, W.R.

(2011) Protein Sci 20: 1929-1934

  • DOI: 10.1002/pro.725
  • Primary Citation of Related Structures:  
    3T43

  • PubMed Abstract: 
  • Methods for rapid and reliable design and structure prediction of linker loops would facilitate a variety of protein engineering applications. Circular permutation, in which the existing termini of a protein are linked by the polypeptide chain and ne ...

    Methods for rapid and reliable design and structure prediction of linker loops would facilitate a variety of protein engineering applications. Circular permutation, in which the existing termini of a protein are linked by the polypeptide chain and new termini are created, is one such application that has been employed for decreasing proteolytic susceptibility and other functional purposes. The length and sequence of the linker can impact the expression level, solubility, structure and function of the permuted variants. Hence it is desirable to achieve atomic-level accuracy in linker design. Here, we describe the use of RosettaRemodel for design and structure prediction of circular permutation linkers on a model protein. A crystal structure of one of the permuted variants confirmed the accuracy of the computational prediction, where the all-atom rmsd of the linker region was 0.89 Å between the model and the crystal structure. This result suggests that RosettaRemodel may be generally useful for the design and structure prediction of protein loop regions for circular permutations or other structure-function manipulations.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV Epitope-Scaffold 4E10_1XIZA_S0_006_CAB162synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.06α = 90
b = 65.27β = 99.57
c = 73.1γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-11-02
    Changes: Database references