1PSV

COMPUTATIONALLY DESIGNED PEPTIDE WITH A BETA-BETA-ALPHA FOLD SELECTION, NMR, 32 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 98 
  • Conformers Submitted: 32 
  • Selection Criteria: NO RESTRAINT VIOLATIONS GREATER THAN 0.3 ANGSTROMS, RMS DEVIATIONS FROM IDEALIZED BOND LENGTHS < 0.01 A, AND RMS DEVIATIONS FROM IDEALIZED ANGLES AND IMPROPERS < 1.0 DEGREE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

De novo protein design: towards fully automated sequence selection.

Dahiyat, B.I.Sarisky, C.A.Mayo, S.L.

(1997) J.Mol.Biol. 273: 789-796

  • DOI: 10.1006/jmbi.1997.1341

  • PubMed Abstract: 
  • Several groups have applied and experimentally tested systematic, quantitative methods to protein design with the goal of developing general design algorithms. We have sought to expand the range of computational protein design by developing quantitat ...

    Several groups have applied and experimentally tested systematic, quantitative methods to protein design with the goal of developing general design algorithms. We have sought to expand the range of computational protein design by developing quantitative design methods for residues of all parts of a protein: the buried core, the solvent exposed surface, and the boundary between core and surface. Our goal is an objective, quantitative design algorithm that is based on the physical properties that determine protein structure and stability and which is not limited to specific folds or motifs. We chose the betabetaalpha motif typified by the zinc finger DNA binding module to test our design methodology. Using previously published sequence scoring functions developed with a combined experimental and computational approach and the Dead-End Elimination theorem to search for the optimal sequence, we designed 20 out of 28 positions in the test motif. The resulting sequence has less than 40% homology to any known sequence and does not contain any metal binding sites or cysteine residues. The resulting peptide, pda8d, is highly soluble and monomeric and circular dichroism measurements showed it to be folded with a weakly cooperative thermal unfolding transition. The NMR solution structure of pda8d was solved and shows that it is well-defined with a backbone ensemble rms deviation of 0. 55 A. Pda8d folds into the desired betabetaalpha motif with well-defined elements of secondary structure and tertiary organization. Superposition of the pda8d backbone to the design target is excellent, with an atomic rms deviation of 1.04 A.


    Related Citations: 
    • De Novo Protein Design: Fully Automated Sequence Selection
      Dahiyat, B.I.,Mayo, S.L.
      (1997) Science 278: 82


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institue of Technology, Pasadena, 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PDA8D
A
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 98 
  • Conformers Submitted: 32 
  • Selection Criteria: NO RESTRAINT VIOLATIONS GREATER THAN 0.3 ANGSTROMS, RMS DEVIATIONS FROM IDEALIZED BOND LENGTHS < 0.01 A, AND RMS DEVIATIONS FROM IDEALIZED ANGLES AND IMPROPERS < 1.0 DEGREE 
  • Olderado: 1PSV Olderado
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance