5DGD | pdb_00005dgd

Benzoylformate decarboxylase F464I and A460V mutant from Pseudomonas putida

• PDB DOI: https://doi.org/10.2210/pdb5DGD/pdb

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


• Deposited: 2015-08-27 Released: 2015-09-16 
• Deposition Author(s): Bera, A.K., Hasson, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Benzoylformate decarboxylase F464I and A460V mutant from Pseudomonas putida

Bera, A.K., Hasson, M.S.

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: 56.56 kDa 
• Atom Count: 4,529 
• Modeled Residue Count: 524 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A	524	Pseudomonas putida	Mutation(s): 2  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	H [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
CA	E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.5	α = 90
b = 95.656	β = 90
c = 137.345	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Bera, A.K., Hasson, M.S.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 2.0: 2021-08-04
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description