7BXR | pdb_00007bxr

2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydroxynorvaline binding form

• PDB DOI: https://doi.org/10.2210/pdb7BXR/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.270 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

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: 90.31 kDa 
• Atom Count: 6,345 
• Modeled 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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F9X (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2S,3R)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-pentanoic acid C13 H21 N2 O8 P BXUMTZWSUSTQMU-MNOVXSKESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.270 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.728	α = 90
b = 101.703	β = 112.911
c = 69.78	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.

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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