1YNO | pdb_00001yno

High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate

• PDB DOI: https://doi.org/10.2210/pdb1YNO/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-01-24 Released: 2006-01-17 
• Deposition Author(s): Bera, A.K., Hasson, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.155 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.152 (DCC) 

Starting Model: experimental

Literature

High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate;

Bera, A.K., Anderson, N.L., 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 56.86 kDa 
• Atom Count: 4,555 
• Modeled Residue Count: 524 
• Deposited Residue Count: 527 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A	527	Pseudomonas putida	Mutation(s): 0  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	F [auth A]	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
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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.155 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.152 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.951	α = 90
b = 95.46	β = 90
c = 136.701	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-17 
Deposition Author(s): Bera, A.K., Hasson, M.S.

Revision History  

• Version 1.0: 2006-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Derived calculations, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description