2FWN

Phosphorylation of an active site serine in a ThDP-dependent enzyme by phosphonate inactivation

• PDB DOI: https://doi.org/10.2210/pdb2FWN/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-02-02 Released: 2006-12-19 
• Deposition Author(s): Bera, A.K., Hasson, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.150 (DCC) 
• R-Value Work: 
  0.140 (DCC) 
• R-Value Observed: 
  0.108 (Depositor) 

Literature

Mechanism-based inactivation of benzoylformate decarboxylase, a thiamin diphosphate-dependent enzyme

Bera, A.K., Polovnikova, L.S., Roestamadji, J., Widlanski, T.S., Kenyon, G.L., McLeish, M.J., Hasson, M.S.

(2007) J Am Chem Soc 129: 4120-4121

• PubMed: 17367138 
• DOI: https://doi.org/10.1021/ja068636z
• Primary Citation of Related Structures:  
  2FWN

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.05 kDa 
• Atom Count: 4,686 
• Modelled Residue Count: 524 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A	528	Pseudomonas putida	Mutation(s): 1  Gene Names: mdlC EC: 4.1.1.7
UniProt
Find proteins for P20906 (Pseudomonas putida) Explore P20906  Go to UniProtKB:  P20906

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	F [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.150 (DCC) 
• R-Value Work:  0.140 (DCC) 
• R-Value Observed: 0.108 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.165	α = 90
b = 95.039	β = 90
c = 137.363	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Bera, A.K., Hasson, M.S.

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2021-08-04
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary