4F4E | pdb_00004f4e

Crystal structure of Aromatic-amino-acid aminotransferase from Burkholderia pseudomallei covalently bound to pyridoxal phosphate

• PDB DOI: https://doi.org/10.2210/pdb4F4E/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia pseudomallei K96243
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-10 Released: 2012-05-23 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Aromatic-amino-acid aminotransferase from Burkholderia pseudomallei covalently bound to pyridoxal phosphate

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Clifton, M.C., Staker, B.L., Myler, P., Stewart, L.J.

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: 91.1 kDa 
• Atom Count: 6,953 
• Modeled Residue Count: 798 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic-amino-acid aminotransferase	A, B	420	Burkholderia pseudomallei K96243	Mutation(s): 0  Gene Names: BPSS0355, tyrB EC: 2.6.1.57 (PDB Primary Data), 2.6.1 (UniProt)
UniProt
Find proteins for Q63NE4 (Burkholderia pseudomallei (strain K96243)) Explore Q63NE4  Go to UniProtKB:  Q63NE4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34F4E

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.92	α = 90
b = 74.82	β = 90
c = 85.28	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2016-05-25
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection