7RU7

Crystal structure of BtrK, a decarboxylase involved in butirosin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb7RU7/pdb

• Classification: LYASE
• Organism(s): Niallia circulans
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-08-16 Released: 2022-08-17 
• Deposition Author(s): Arenas, L.A.R., Paiva, F.C.R., Huang, F., Leadlay, P., Dias, M.V.B.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Crystal structure of BtrK, a decarboxylase involved in the (S)-4-amino-2-hydroxybutyrate (AHBA) formation during butirosin biosynthesis

Rivas Arenas, L.A., de Paiva, F.C., de O.Rossini, N., Li, Y., Spencer, J., Leadlay, P., Dias, M.V.

(2022) J Mol Struct 1267: 133576

• DOI: https://doi.org/10.1016/j.molstruc.2022.133576

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.4 kDa 
• Atom Count: 3,648 
• Modelled Residue Count: 412 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-glutamyl-[BtrI acyl-carrier protein] decarboxylase	A	448	Niallia circulans	Mutation(s): 0  Gene Names: btrK EC: 4.1.1.95
UniProt
Find proteins for Q2L4H3 (Niallia circulans) Explore Q2L4H3  Go to UniProtKB:  Q2L4H3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PEG (Subject of Investigation/LOI)	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.912	α = 90
b = 129.544	β = 90
c = 45.721	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-17 
Deposition Author(s): Arenas, L.A.R., Paiva, F.C.R., Huang, F., Leadlay, P., Dias, M.V.B.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	18/00351-1

Revision History  

• Version 1.0: 2022-08-17
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description