3ODD

Comparison of the character and the speed of X-ray-induced structural changes of porcine pancreatic elastase at two temperatures, 100 and 15K. The data set was collected from region B of the crystal. Second step of radiation damage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

X-ray-induced deterioration of disulfide bridges at atomic resolution.

Petrova, T.Ginell, S.Mitschler, A.Kim, Y.Lunin, V.Y.Joachimiak, G.Cousido-Siah, A.Hazemann, I.Podjarny, A.Lazarski, K.Joachimiak, A.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1075-1091

  • DOI: https://doi.org/10.1107/S0907444910033986
  • Primary Citation of Related Structures:  
    3MNB, 3MNC, 3MNS, 3MNX, 3MO3, 3MO6, 3MO9, 3MOC, 3MTY, 3MU0, 3MU1, 3MU4, 3MU5, 3MU8, 3ODD, 3ODF

  • PubMed Abstract: 

    Overall and site-specific X-ray-induced damage to porcine pancreatic elastase was studied at atomic resolution at temperatures of 100 and 15 K. The experiments confirmed that irradiation causes small movements of protein domains and bound water molecules in protein crystals. These structural changes occur not only at 100 K but also at temperatures as low as 15 K. An investigation of the deterioration of disulfide bridges demonstrated the following. (i) A decrease in the occupancy of S(γ) atoms and the appearance of new cysteine rotamers occur simultaneously. (ii) The occupancy decrease is observed for all S(γ) atoms, while new rotamers arise for some of the cysteine residues; the appearance of new conformations correlates with the accessibility to solvent. (iii) The sum of the occupancies of the initial and new conformations of a cysteine residue is approximately equal to the occupancy of the second cysteine residue in the bridge. (iv) The most pronounced changes occur at doses below 1.4 × 10(7) Gy, with only small changes occurring at higher doses. Comparison of the radiation-induced changes in an elastase crystal at 100 and 15 K suggested that the dose needed to induce a similar level of deterioration of the disulfide bonds and atomic displacements at 15 K to those seen at 100 K is more than two times higher.


  • Organizational Affiliation

    Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chymotrypsin-like elastase family member 1240Sus scrofaMutation(s): 0 
EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa)
Explore P00772 
Go to UniProtKB:  P00772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00772
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.987α = 90
b = 57.778β = 90
c = 74.585γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
AMoREphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description