4TM5 | pdb_00004tm5

X-ray crystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264 bound to the co-factor pyridoxal phosphate

• PDB DOI: https://doi.org/10.2210/pdb4TM5/pdb

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


• Deposited: 2014-05-31 Released: 2014-07-02 
• Deposition Author(s): Fairman, J.W., Taylor, B.M., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

X-ray crystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264 bound to the co-factor pyridoxal phosphate

Fairman, J.W., Taylor, B.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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,648 
• Modeled Residue Count: 296 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-amino acid aminotransferase	A	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

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: 1.60 Å
• R-Value Free:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34TM5

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.83	α = 90
b = 70.02	β = 90
c = 140.01	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Fairman, J.W., Taylor, B.M., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 2.0: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary
• Version 2.1: 2019-12-11
  Changes: Author supporting evidence
• Version 2.2: 2023-12-27
  Changes: Data collection, Database references, Refinement description