9J0V

Crystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in P 21 21 21 space group

• PDB DOI: https://doi.org/10.2210/pdb9J0V/pdb

• Classification: TRANSFERASE
• Organism(s): Desulfobacula toluolica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-03 Released: 2024-09-18 
• Deposition Author(s): Matyuta, I.O., Bakunova, A.K., Nikolaeva, A.Y., Rakitina, T.V., Bezsudnova, E.Y., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: in silico

Literature

From Structure to Function: Analysis of the First Monomeric Pyridoxal-5'-Phosphate-Dependent Transaminase from the Bacterium Desulfobacula toluolica

Bakunova, A.K., Matyuta, I.O., Nikolaeva, A.Y., Rakitina, T.V., Boyko, K.M., Popov, V.O., Bezsudnova, E.Y.

(2024) Biomolecules 14

• DOI: https://doi.org/10.3390/biom14121591

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.48 kDa 
• Atom Count: 2,002 
• Modelled Residue Count: 246 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dat: predicted D-alanine aminotransferase	A	286	Desulfobacula toluolica	Mutation(s): 0  Gene Names: dat, TOL2_C39420 EC: 2.6.1.21
UniProt
Find proteins for K0NPP0 (Desulfobacula toluolica (strain DSM 7467 / Tol2)) Explore K0NPP0  Go to UniProtKB:  K0NPP0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.847	α = 90
b = 56.226	β = 90
c = 118.625	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Matyuta, I.O., Bakunova, A.K., Nikolaeva, A.Y., Rakitina, T.V., Bezsudnova, E.Y., Popov, V.O., Boyko, K.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release
  
• Version 2.0: 2024-12-25
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary