4TVI | pdb_00004tvi

X-ray crystal structure of an aminotransferase from Brucella abortus bound to the co-factor PLP

• PDB DOI: https://doi.org/10.2210/pdb4TVI/pdb

• Classification: TRANSFERASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-27 Released: 2014-07-30 
• Deposition Author(s): 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: 2.10 Å
• R-Value Free: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of an aminotransferase from Brucella abortus bound to the co-factor PLP

Fairman, J.W., Davies, D.R., Lorimer, D., Edwards, T.E.

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: 69.75 kDa 
• Atom Count: 4,868 
• Modeled Residue Count: 560 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase, class IV	A, B	312	Brucella abortus 2308	Mutation(s): 0  Gene Names: BAB2_0572 EC: 2.6.1.42
UniProt
Find proteins for Q2YKS6 (Brucella abortus (strain 2308)) Explore Q2YKS6  Go to UniProtKB:  Q2YKS6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [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: 2.10 Å
• R-Value Free:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34TVI

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.99	α = 90
b = 127.32	β = 90
c = 47.69	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): 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: 2014-07-30
  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: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 2.3: 2023-11-15
  Changes: Data collection
• Version 2.4: 2025-10-22
  Changes: Structure summary