1EGV

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSELLA OXYTOCA UNDER THE ILLUMINATED CONDITION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

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This is version 1.3 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: 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 ...

    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.


    Related Citations: 
    • A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase
      Shibata, N., Masuda, J., Toraya, T., Morimoto, Y., Yasuoka, N.
      (1999) Structure 7: 997

    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASEA, D [auth L]554Klebsiella oxytocaMutation(s): 0 
Gene Names: pddApduCAB185_12495AGF18_15670C2U42_33605C2U44_05475SAMEA2273575_05741
EC: 4.2.1.28
UniProt
Find proteins for Q59470 (Klebsiella oxytoca)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASEB, E224Klebsiella oxytocaMutation(s): 0 
Gene Names: pddB
EC: 4.2.1.28
UniProt
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASEC [auth G], F [auth M]173Klebsiella oxytocaMutation(s): 0 
Gene Names: pddCpduEAB185_12485C2U42_33595
EC: 4.2.1.28
UniProt
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.38α = 90
b = 121.4β = 90
c = 207.6γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-21
    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