9J0U

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


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dat: predicted D-alanine aminotransferase286Desulfobacula toluolicaMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK0NPP0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
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 = 250.089α = 90
b = 250.089β = 90
c = 250.089γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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