1EEX

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

• PDB DOI:  https://doi.org/10.2210/pdb1EEX/pdb

• Classification: LYASE
• Organism(s): Klebsiella oxytoca
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-02-04 Released: 2001-02-07 
• Deposition Author(s): Shibata, N., Masuda, J., Toraya, T., Morimoto, Y., Yasuoka, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.226 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 

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

• PubMed: 10903944 
• 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 210.88 kDa 
• Atom Count: 15,494 
• Modelled Residue Count: 1,732 
• Deposited Residue Count: 1,902 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROPANEDIOL DEHYDRATASE	A, D [auth L]	554	Klebsiella oxytoca	Mutation(s): 0  Gene Names: pddA EC: 4.2.1.28
UniProt
Find proteins for Q59470 (Klebsiella oxytoca) Explore Q59470  Go to UniProtKB:  Q59470

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROPANEDIOL DEHYDRATASE	B, E	224	Klebsiella oxytoca	Mutation(s): 0  Gene Names: pddB EC: 4.2.1.28
UniProt
Find proteins for Q59471 (Klebsiella oxytoca) Explore Q59471  Go to UniProtKB:  Q59471

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROPANEDIOL DEHYDRATASE	C [auth G], F [auth M]	173	Klebsiella oxytoca	Mutation(s): 0  Gene Names: pddC, DVB85_01585 EC: 4.2.1.28
UniProt
Find proteins for Q59472 (Klebsiella oxytoca) Explore Q59472  Go to UniProtKB:  Q59472

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COY	I [auth A], M [auth L]	CO-(ADENIN-9-YL-PENTYL)-COBALAMIN C72 H106 Co N18 O14 P KWGNLVVAVJCVFN-AFACOYQJDT
PGO	J [auth A], N [auth L]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
K	G [auth A], H [auth A], K [auth L], L	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.226 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.38	α = 90
b = 121.4	β = 90
c = 207.6	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-07 
Deposition Author(s): Shibata, N., Masuda, J., Toraya, T., Morimoto, Y., Yasuoka, N.

Revision History  

• Version 1.0: 2001-02-07
  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