9J0U

Crystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in F 41 3 2 space group

PDB DOI: https://doi.org/10.2210/pdb9J0U/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.253
R-Value Work: 0.209
R-Value Observed: 0.211

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

High/low resolution monomeric PLP-dependent transaminase from Desulfobacula toluolica

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

To be published.

Macromolecule Content

Total Structure Weight: 32.3 kDa
Atom Count: 2,268
Modelled Residue Count: 286
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dat: predicted D-alanine aminotransferase	A	286	Desulfobacula toluolica	Mutation(s): 0 EC: 2.6.1.21
UniProt
Find proteins for K0NPP0 (Desulfobacula toluolica (strain DSM 7467 / Tol2)) Explore K0NPP0 Go to UniProtKB: K0NPP0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K0NPP0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.253
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 250.089	α = 90
b = 250.089	β = 90
c = 250.089	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-18

Deposition Author(s):

Nikolaeva, A.Y.

Bezsudnova, E.Y.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-09-18
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.