3AL1

DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.75 Å
  • R-Value Free: 0.145 
  • R-Value Observed: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.

Patterson, W.R.Anderson, D.H.DeGrado, W.F.Cascio, D.Eisenberg, D.

(1999) Protein Sci 8: 1410-1422

  • DOI: 10.1110/ps.8.7.1410
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We report the 0.75 A crystal structure of a racemic mixture of the 12-residue designed peptide "Alpha-1" (Acetyl-ELLKKLLEELKG), the L-enantiomer of which is described in the accompanying paper. Equivalent solutions of the centrosymmetric bilayers wer ...

    We report the 0.75 A crystal structure of a racemic mixture of the 12-residue designed peptide "Alpha-1" (Acetyl-ELLKKLLEELKG), the L-enantiomer of which is described in the accompanying paper. Equivalent solutions of the centrosymmetric bilayers were determined by two direct phasing programs in space groups P1 and P1bar. The unit cell contains two L-alpha-helices and two D-alpha-helices. The columnar-sheet bilayer motif seen in L-Alpha-1 is maintained in the D,L-Alpha-1 structure except that each sheet of head-to-tail helices is composed of one enantiomer and is related to its neighboring sheets by inversion symmetry. Comparison to the L-Alpha-1 structure provides further insight into peptide design. The high resolution and small asymmetric unit allowed building an intricate model (R = 13.1%, Rfree = 14.5%) that incorporates much of the discrete disorder of peptide and solvent. Ethanolamine and 2-methyl-2,4-pentanediol (MPD) molecules bind near helix termini. Rigid body analysis identifies sites of restricted displacements and torsions. Side-chain discrete disorder propagates into the backbone of one helix but not the other. Although no side chain in Alpha-1 is rigid, the environments in the crystal restrict some of them to no or only one active torsion.


    Related Citations: 
    • Packed Protein Bilayers in the 0.90A Resolution Structure of a Designed Alpha Helical Bundle
      Prive, G.G., Anderson, D.H., Wesson, L., Cascio, D., Eisenberg, D.
      () To be published --: --
    • Crystal Structure of Alpha-1: Implications for Protein Design
      Hill, C.P., Anderson, D.H., Wesson, L., Degrado, W.F., Eisenberg, D.
      (1990) Science 249: 543
    • The Design, Synthesis, and Crystallization of an Alpha-Helical Peptide
      Eisenberg, D., Wilcox, W., Eshita, S.M., Pryciak, P.M., Ho, S.P.
      (1986) Proteins 1: 16

    Organizational Affiliation

    Molecular Biology Institute at UCLA and the Department of Chemistry and Biochemistry, University of California, Los Angeles 90095-1570, USA.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (D, L-ALPHA-1)
A, B
13N/AMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ETA
Query on ETA

Download CCD File 
B
ETHANOLAMINE
C2 H7 N O
HZAXFHJVJLSVMW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.75 Å
  • R-Value Free: 0.145 
  • R-Value Observed: 0.130 
  • Space Group: P -1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 20.544α = 101.16
b = 20.859β = 97.03
c = 26.055γ = 118.06
Software Package:
Software NamePurpose
SHELXSphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-03-28
    Changes: Other