6A50 | pdb_00006a50

structure of benzoylformate decarboxylases in complex with cofactor TPP

• PDB DOI: https://doi.org/10.2210/pdb6A50/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-21 Released: 2019-02-20 
• Deposition Author(s): Guo, Y., Wang, S., Nie, Y., Li, S.
• Funding Organization(s): Chinese Academy of Sciences, National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

A Synthetic Pathway for Acetyl-Coenzyme A Biosynthesis

Lu, X., Liu, Y., Yang, Y., Wang, S., Wang, Q., Wang, X., Yan, Z., Cheng, J., Liu, C., Yang, X., Luo, H., Yang, S., Gou, J., Ye, L., Lu, L., Zhang, Z., Guo, Y., Nie, Y., Lin, J., Li, S., Cai, T., Ma, H., Wang, W., Liu, Y., Li, Y., Jiang, H., Tian, C.

(2019) Nat Commun 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 118.25 kDa 
• Atom Count: 8,988 
• Modeled Residue Count: 1,054 
• Deposited Residue Count: 1,098 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
benzoylformate decarboxylases	A, B	549	Pseudomonas putida	Mutation(s): 0  EC: 4.1.1.7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.889	α = 90
b = 124.392	β = 122.35
c = 97.758	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Guo, Y., Wang, S., Nie, Y., Li, S.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	ZDRW-ZS-2016
National Basic Research Program of China (973 Program)	China	2015CB755704

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description