4M0J | pdb_00004m0j

Crystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264

• PDB DOI: https://doi.org/10.2210/pdb4M0J/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia thailandensis E264
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-01 Released: 2013-10-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264

Lukacs, C.M., Edwards, T.E., Lorimer, D.

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)

Macromolecule Content 

• Total Structure Weight: 68.07 kDa 
• Atom Count: 4,538 
• Modeled Residue Count: 571 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-amino acid aminotransferase	A, B	311	Burkholderia thailandensis E264	Mutation(s): 0  Gene Names: BTH_I0381
UniProt
Find proteins for Q2T1L0 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T1L0  Go to UniProtKB:  Q2T1L0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34M0J

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.6	α = 90
b = 73.98	β = 105.35
c = 76.21	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-10-22
  Changes: Structure summary