2VBI

Holostructure of pyruvate decarboxylase from Acetobacter pasteurianus

• PDB DOI: https://doi.org/10.2210/pdb2VBI/pdb

• Classification: LYASE
• Organism(s): Acetobacter pasteurianus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-09-14 Released: 2008-04-08 
• Deposition Author(s): Gocke, D., Berthold, C.L., Schneider, G., Pohl, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.243 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 493.14 kDa 
• Atom Count: 33,860 
• Modelled Residue Count: 4,432 
• Deposited Residue Count: 4,528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE DECARBOXYLASE	A, B, C, D, E, F, G, H	566	Acetobacter pasteurianus	Mutation(s): 0  EC: 4.1.1.1
UniProt
Find proteins for Q8L388 (Acetobacter pasteurianus) Explore Q8L388  Go to UniProtKB:  Q8L388

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
MG	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.243 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.619	α = 90
b = 162.434	β = 102.71
c = 169.331	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: 2008-04-08 
Deposition Author(s): Gocke, D., Berthold, C.L., Schneider, G., Pohl, M.

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description