4K9Q | pdb_00004k9q

The Crystal Structure of Benzoylformate Decarboxylase from Polynucleobacter necessarius

• PDB DOI: https://doi.org/10.2210/pdb4K9Q/pdb

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


• Deposited: 2013-04-20 Released: 2014-04-23 
• Deposition Author(s): Brodkin, H.R., Novak, W.R.P., McLeish, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Benzoylformate Decarboxylase from Polynucleobacter necessarius

Brodkin, H.R., Andrews, F.H., Novak, W.R.P., Petsko, G.A., Ringe, D., McLeish, M.J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 119.79 kDa 
• Atom Count: 9,452 
• Modeled Residue Count: 1,061 
• Deposited Residue Count: 1,078 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate Decarboxylase	A, B	539	Polynucleobacter necessarius	Mutation(s): 0  Gene Names: Pnuc_1088 EC: 4.1.1.7
UniProt
Find proteins for A4SXU0 (Polynucleobacter asymbioticus (strain DSM 18221 / CIP 109841 / QLW-P1DMWA-1)) Explore A4SXU0  Go to UniProtKB:  A4SXU0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.737	α = 90
b = 104.953	β = 90
c = 158.731	γ = 90

Software Package:

Software Name	Purpose
BlueIce-Epics	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Brodkin, H.R., Novak, W.R.P., McLeish, M.J.

Revision History  

• Version 1.0: 2014-04-23
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description