1EJG | pdb_00001ejg

CRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY.

• PDB DOI: https://doi.org/10.2210/pdb1EJG/pdb

• Classification: PLANT PROTEIN
• Organism(s): Crambe hispanica subsp. abyssinica
• Mutation(s): Yes 


• Deposited: 2000-03-02 Released: 2000-04-05 
• Deposition Author(s): Jelsch, C., Teeter, M.M., Lamzin, V., Pichon-Lesme, V., Blessing, B., Lecomte, C.

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Experimental Data Snapshot

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

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

• PubMed: 10737790 
• DOI: https://doi.org/10.1073/pnas.97.7.3171
• Primary Citation 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 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.74 kDa 
• Atom Count: 424 
• Modeled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRAMBIN (PRO22,SER22/LEU25,ILE25)	A	46	Crambe hispanica subsp. abyssinica	Mutation(s): 2
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica) Explore P01542  Go to UniProtKB:  P01542

Experimental Data & Validation

Experimental Data

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

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.824	α = 90
b = 18.498	β = 90.47
c = 22.371	γ = 90

Software Package:

Software Name	Purpose
DREAR	data reduction
MOLLY	refinement
DREAR	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-05 
Deposition Author(s): Jelsch, C., Teeter, M.M., Lamzin, V., Pichon-Lesme, V., Blessing, B., Lecomte, C.

Revision History  

• 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
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Structure summary