7BXP

2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator

• PDB DOI: https://doi.org/10.2210/pdb7BXP/pdb

• Classification: LIGASE,TRANSFERASE
• Organism(s): Cupriavidus necator
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-20 Released: 2021-04-21 
• Deposition Author(s): Motoyama, T., Nakano, S., Hasebe, F., Miyoshi, N., Ito, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase

Motoyama, T., Nakano, S., Hasebe, F., Miyata, R., Kumazawa, S., Miyoshi, N., Ito, S.

(2021) Commun Chem 4: 108-108

• DOI: https://doi.org/10.1038/s42004-021-00545-8

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 90.16 kDa 
• Atom Count: 7,000 
• Modelled Residue Count: 798 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-3-ketobutyrate coenzyme A ligase	A, B	411	Cupriavidus necator	Mutation(s): 0  Gene Names: kbl, H16_B0819 EC: 2.3.1.29
UniProt
Find proteins for Q0K313 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore Q0K313  Go to UniProtKB:  Q0K313

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.376	α = 90
b = 105.847	β = 105.791
c = 67.744	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Motoyama, T., Nakano, S., Hasebe, F., Miyoshi, N., Ito, S.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K14391
Japan Society for the Promotion of Science (JSPS)	Japan	19J23697

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description