1EGM

CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

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This is version 2.1 of the entry. See complete history. 


Literature

How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.

Masuda, J., Shibata, N., Morimoto, Y., Toraya, T., Yasuoka, N.

(2000) Structure 8: 775-788

  • DOI: https://doi.org/10.1016/s0969-2126(00)00164-7
  • Primary Citation of Related Structures:  
    1EEX, 1EGM, 1EGV

  • PubMed Abstract: 

    Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved.

    • Organizational Affiliation: 

    Department of Life Science, Himeji Institute of Technology, Kamigori, Akogun, 678-1297, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASEA,
D [auth L]		554Klebsiella oxytocaMutation(s): 0 
EC: 4.2.1.28
UniProt
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UniProt GroupQ59470
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASE
B, E
224Klebsiella oxytocaMutation(s): 0 
EC: 4.2.1.28
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASEC [auth G],
F [auth M]		173Klebsiella oxytocaMutation(s): 0 
EC: 4.2.1.28
UniProt
Find proteins for Q59472 (Klebsiella oxytoca)
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Entity Groups  
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UniProt GroupQ59472
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74α = 90
b = 121.6β = 90
c = 207.7γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 2.0: 2021-08-18
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-07
    Changes: Data collection