8PNX

Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens in PMP form

• PDB DOI: https://doi.org/10.2210/pdb8PNX/pdb

• Classification: TRANSFERASE
• Organism(s): Blastococcus saxobsidens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-03 Released: 2024-07-10 
• Deposition Author(s): Matyuta, I.O., Boyko, K.M., Nikolaeva, A.Y., Shilova, S.A., Popov, V.O.
• Funding Organization(s): Russian Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structural determinants of dual substrate recognition in the transaminase from Blastococcus saxobsidens specific to D-amino acids and R-amines

Shilova, S.A., Nikolaeva, A.Y., Matyuta, I.O., Boyko, K.M., Popov, V.O., Bezsudnova, E.Y.

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

Macromolecule Content

• Total Structure Weight: 29.38 kDa 
• Atom Count: 2,366 
• Modelled Residue Count: 278 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase	A	281	Blastococcus saxobsidens	Mutation(s): 0  Gene Names: BLASA_4517
UniProt
Find proteins for H6RQF3 (Blastococcus saxobsidens (strain DD2)) Explore H6RQF3  Go to UniProtKB:  H6RQF3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP (Subject of Investigation/LOI)	B [auth A]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.437	α = 90
b = 105.437	β = 90
c = 51.144	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Matyuta, I.O., Boyko, K.M., Nikolaeva, A.Y., Shilova, S.A., Popov, V.O.

---

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	19-14-00164

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release