1EJG

CRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.54 Å
  • R-Value Free: 0.094 
  • R-Value Work: 0.090 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.

Jelsch, C.Teeter, M.M.Lamzin, V.Pichon-Pesme, V.Blessing, R.H.Lecomte, C.

(2000) Proc Natl Acad Sci U S A 97: 3171-3176

  • DOI: 10.1073/pnas.97.7.3171
  • Primary Citation of Related Structures:  
    1EJG

  • PubMed Abstract: 
  • The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution ...

    The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.


    Organizational Affiliation

    Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, Université Henri Poincaré-Nancy 1-Centre National de la Recherche Scientifique ESA 7036, BP 239, 54506 Vandoeuvre-lès-Nancy, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRAMBIN (PRO22,SER22/LEU25,ILE25)A46Crambe hispanica subsp. abyssinicaMutation(s): 2 
Gene Names: THI2
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica)
Explore P01542 
Go to UniProtKB:  P01542
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01542
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.54 Å
  • R-Value Free: 0.094 
  • R-Value Work: 0.090 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.824α = 90
b = 18.498β = 90.47
c = 22.371γ = 90
Software Package:
Software NamePurpose
DREARdata reduction
MOLLYrefinement
DREARdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.3: 2014-02-05
    Changes: Other
  • Version 1.4: 2017-10-04
    Changes: Refinement description