9F3Y

CutC choline lyase in complex with difluorocholine

• PDB DOI: https://doi.org/10.2210/pdb9F3Y/pdb

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


• Deposited: 2024-04-26 Released: 2024-05-08 
• Deposition Author(s): Kalnins, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.295 
• R-Value Work: 0.220 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

CutC choline lyase in complex with difluorocholine

Kalnins, G.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 1,027.78 kDa 
• Atom Count: 50,317 
• Modelled Residue Count: 6,336 
• Deposited Residue Count: 9,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline trimethylamine-lyase	A, B, C, D, E, F, G, H	1,150	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: hpdB, cutC, SAMEA4873561_02933, SAMEA4873648_04511 EC: 4.3.99.4
UniProt
Find proteins for A0A486V7R5 (Klebsiella pneumoniae) Explore A0A486V7R5  Go to UniProtKB:  A0A486V7R5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H9L (Subject of Investigation/LOI)	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	difluorocholine C5 H12 F2 N YOGYDOVCYPFAGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.295 
• R-Value Work: 0.220 
• R-Value Observed: 0.224 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.366	α = 77.65
b = 117.573	β = 85.337
c = 212.531	γ = 70.007

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Kalnins, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release