4K9N | pdb_00004k9n

Crystal Structure of the Ala460Ile mutant of Benzoylformate Decarboxylase from Pseudomonas putida

• PDB DOI: https://doi.org/10.2210/pdb4K9N/pdb

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


• Deposited: 2013-04-20 Released: 2013-05-08 
• Deposition Author(s): Brodkin, H.R., McLeish, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Ala460Ile mutant of Benzoylformate Decarboxylase from Pseudomonas putida

Brodkin, H.R., Andrews, F.H., Milne, A.C., 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: 229.27 kDa 
• Atom Count: 17,652 
• Modeled Residue Count: 2,096 
• Deposited Residue Count: 2,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A, B, C, D	530	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
TZD	G [auth A], J [auth B], L [auth C], O [auth D]	2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE C12 H18 N4 O8 P2 S ZGJUYGIRPQSCFA-UHFFFAOYSA-N
GOL	M [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.637	α = 90
b = 163.499	β = 90
c = 175.502	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: 2013-05-08 
Deposition Author(s): Brodkin, H.R., McLeish, M.J.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description