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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 Fold.Des. 8: 775-788

  • Primary Citation of Related Structures:  

  • 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 cleavag ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROPANEDIOL DEHYDRATASE
A, L
554Klebsiella oxytocaMutation(s): 0 
Gene Names: pddA (pduC)
EC: 4.2.1.28
Find proteins for Q59470 (Klebsiella oxytoca)
Go to UniProtKB:  Q59470
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROPANEDIOL DEHYDRATASE
B, E
224Klebsiella oxytocaMutation(s): 0 
Gene Names: pddB (pduD)
EC: 4.2.1.28
Find proteins for Q59471 (Klebsiella oxytoca)
Go to UniProtKB:  Q59471
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROPANEDIOL DEHYDRATASE
G, M
173Klebsiella oxytocaMutation(s): 0 
Gene Names: pddC (pduE)
EC: 4.2.1.28
Find proteins for Q59472 (Klebsiella oxytoca)
Go to UniProtKB:  Q59472
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, L
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CNC
Query on CNC

Download SDF File 
Download CCD File 
A, L
CO-CYANOCOBALAMIN
C63 H88 Co N14 O14 P
OEEKSCBDGPRZJZ-BYLSPCLQSA-N
 Ligand Interaction
PGO
Query on PGO

Download SDF File 
Download CCD File 
A, L
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.000α = 90.00
b = 121.600β = 90.00
c = 207.700γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
CCP4data scaling
MOSFLMdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance