4MPJ | pdb_00004mpj

Phosphorylation of an active site threonine in the benzyolformate decarboxylase mutant S26T by phosphonate inactivation

• PDB DOI: https://doi.org/10.2210/pdb4MPJ/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-09-12 Released: 2015-03-18 
• Deposition Author(s): Andrews, F.H., McLeish, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.142 (Depositor), 0.143 (DCC) 
• R-Value Work: 
  0.118 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.119 (Depositor) 

Literature

Phosphorylation of an active site threonine in the benzyolformate decarboxylase mutant S26T by phosphonate inactivation

Andrews, F.H., 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: 58.41 kDa 
• Atom Count: 4,745 
• Modeled Residue Count: 525 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A	536	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	E [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.142 (Depositor), 0.143 (DCC) 
• R-Value Work:  0.118 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.119 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.254	α = 90
b = 95.343	β = 90
c = 137.114	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Andrews, F.H., McLeish, M.J.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary