Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 119.48 kDa 
• Atom Count: 9,847 
• Modelled Residue Count: 1,098 
• Deposited Residue Count: 1,116 
• Unique protein chains: 1

 4COK

Functional and Structural Characterization of Pyruvate decarboxylase from Gluconoacetobacter diazotrophicus

• PDB DOI: 10.2210/pdb4COK/pdb

• Classification: LYASE
• Organism(s): Gluconacetobacter diazotrophicus PA1 5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-29 Released: 2014-10-01 
• Deposition Author(s): vanZyl, L.J., Schubert, W.-D., Tuffin, M., Cowan, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.163 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 

Literature

Structure and Functional Characterization of Pyruvate Decarboxylase from Gluconacetobacter Diazotrophicus.

Van Zyl, L.J., Schubert, W., Tuffin, M.I., Cowan, D.A.

(2014) BMC Struct Biol 14: 21

• PubMed: 25369873 
• DOI: 10.1186/s12900-014-0021-1
• Primary Citation of Related Structures:  
  4COK


• PubMed Abstract: 
  

Bacterial pyruvate decarboxylases (PDC) are rare. Their role in ethanol production and in bacterially mediated ethanologenic processes has, however, ensured a continued and growing interest. PDCs from Zymomonas mobilis (ZmPDC), Zymobacter palmae (ZpPDC) and Sarcina ventriculi (SvPDC) have been characterized and ZmPDC has been produced successfully in a range of heterologous hosts. PDCs from the Acetobacteraceae and their role in metabolism have not been characterized to the same extent. Examples include Gluconobacter oxydans (GoPDC), G. diazotrophicus (GdPDC) and Acetobacter pasteutrianus (ApPDC). All of these organisms are of commercial importance.

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Organizational Affiliation: 

Department of Genetics, University of Pretoria, Pretoria, 0002, South Africa. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE DECARBOXYLASE	A, B	558	Gluconacetobacter diazotrophicus PA1 5	Mutation(s): 0  Gene Names: pdc, GDI0172 EC: 4.1.1.1
UniProt
Find proteins for A9H275 (Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / CCUG 37298 / CIP 103539 / LMG 7603 / PAl5)) Explore A9H275  Go to UniProtKB:  A9H275

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	C [auth A], G [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.163 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.07	α = 90
b = 140.96	β = 125.78
c = 91.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): vanZyl, L.J., Schubert, W.-D., Tuffin, M., Cowan, D.A.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2015-04-08
  Changes: Database references