X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin with a Cubic Space Group

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis.

Bang, D.Gribenko, A.V.Tereshko, V.Kossiakoff, A.A.Kent, S.B.Makhatadze, G.I.

(2006) Nat Chem Biol 2: 139-143

  • DOI: https://doi.org/10.1038/nchembio766
  • Primary Citation of Related Structures:  
    2FCM, 2FCN, 2FCQ, 2FCS

  • PubMed Abstract: 

    The alpha-helix is a fundamental protein structural motif and is frequently terminated by a glycine residue. Explanations for the predominance of glycine at the C-cap terminal portions of alpha-helices have invoked uniquely favorable energetics of this residue in a left-handed conformation or enhanced solvation of the peptide backbone because of the absence of a side chain. Attempts to quantify the contributions of these two effects have been made previously, but the issue remains unresolved. Here we have used chemical protein synthesis to dissect the energetic basis of alpha-helix termination by comparing a series of ubiquitin variants containing an L-amino acid or the corresponding D-amino acid at the C-cap Gly35 position. D-Amino acids can adopt a left-handed conformation without energetic penalty, so the contributions of conformational strain and backbone solvation can thus be separated. Analysis of the thermodynamic data revealed that the preference for glycine at the C' position of a helix is predominantly a conformational effect.

  • Organizational Affiliation

    Institute for Biophysical Dynamics, Center for Integrative Science, 929 East 57th Street, The University of Chicago, Chicago, Illinois 60637, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
76N/AMutation(s): 2 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]
E [auth A]
F [auth A]
H [auth A]
I [auth A]
C [auth A],
E [auth A],
F [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
G [auth A]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.254 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.532α = 90
b = 105.532β = 90
c = 105.532γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description