4ICB

PROLINE CIS-TRANS ISOMERS IN CALBINDIN D9K OBSERVED BY X-RAY CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography.

Svensson, L.A.Thulin, E.Forsen, S.

(1992) J Mol Biol 223: 601-606

  • DOI: https://doi.org/10.1016/0022-2836(92)90976-q
  • Primary Citation of Related Structures:  
    4ICB

  • PubMed Abstract: 

    In a structure of recombinant bovine calbindin D9k, determined crystallographically to 1.6 A resolution, a proline in mixed, approximately equally populated, cis and trans conformation is observed. Isomers of this kind have not been reported in structure determinations of calbindin D9k to 2.3 A resolution or in any other crystallographically determined protein structure. The cis-trans isomerization occurs at the peptide bond between Gly42 and Pro43, which is in agreement with results from two-dimensional 1H nuclear magnetic resonance spectroscopy experiments on solutions of calbindin D9k. Alternative backbone stretches have been modeled and refined by stereochemical restrained least-squares refinement for the segment Lys41 to Pro43. The final R-value was 0.188. The structural perturbations accompanying the cis-trans isomerization are found to be very localized. The largest positional differences are observed at residue Gly42, in which the alternative positions of the oxygen atom are 3.6 A apart.


  • Organizational Affiliation

    Department of Molecular Biophysics, University of Lund, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CALBINDIN D9K76Bos taurusMutation(s): 0 
UniProt
Find proteins for P02633 (Bos taurus)
Explore P02633 
Go to UniProtKB:  P02633
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02633
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.13α = 90
b = 43β = 90
c = 29.32γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-02-12
    Changes: Version format compliance
  • Version 1.4: 2019-07-17
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-02-28
    Changes: Data collection, Database references, Derived calculations