6WNN | pdb_00006wnn

Bacillus subtilis BioA in complex with amino donor L-Lys

• PDB DOI: https://doi.org/10.2210/pdb6WNN/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-22 Released: 2021-04-28 
• Deposition Author(s): Souza, S.A., Ng, H.L.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.333 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Substrate divergence in 7,8-diaminopelargonic acid synthesis: mutagenesis and computational studies of L-lysine dependent Bacillus subtilis BioA

Cramer, J., Kubota, C., Souza, S.A., Morris, J., Ng, H.L., Sun, R., Jarrett, J.T.

To be published.

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: 102.63 kDa 
• Atom Count: 6,618 
• Modeled Residue Count: 836 
• Deposited Residue Count: 908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase	A, B	454	Bacillus subtilis	Mutation(s): 0  Gene Names: bioA, A3772_16240, B4417_0368 EC: 2.6.1.62 (PDB Primary Data), 2.6.1.105 (UniProt)
UniProt
Find proteins for P53555 (Bacillus subtilis (strain 168)) Explore P53555  Go to UniProtKB:  P53555

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLP (Subject of Investigation/LOI)	C [auth A]	(2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid C14 H22 N3 O7 P YQSOQJORMNSDJL-QFULYMJESA-N
PMP	D [auth B]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.333 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.3	α = 96.15
b = 60.54	β = 106.04
c = 62.72	γ = 99.23

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Souza, S.A., Ng, H.L.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1833181

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection