4XJL

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a HTS lead compound

• PDB DOI: https://doi.org/10.2210/pdb4XJL/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-08 Released: 2016-01-20 
• Deposition Author(s): Finzel, B.C., Dai, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.214 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Fragment based inhibitor design of Mycobacterium tuberculosis BioA (http://hdl.handle.net/11299/171084)

Dai, R.

(2015) Thesis 

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: 98.5 kDa 
• Atom Count: 6,893 
• Modelled Residue Count: 858 
• Deposited Residue Count: 914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase	A, B	457	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: bioA, Rv1568, MTCY336.35c EC: 2.6.1.62
UniProt
Find proteins for P9WQ81 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQ81  Go to UniProtKB:  P9WQ81

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
41F	E [auth B], F [auth B]	N-(1,2,3-benzothiadiazol-5-yl)-4-phenylpiperazine-1-carboxamide C17 H17 N5 O S FFLVDHOMQBCRBY-UHFFFAOYSA-N
PLP	D [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.214 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.294	α = 90
b = 66.008	β = 90
c = 203.634	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Finzel, B.C., Dai, R.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-02-03
  Changes: Database references
• Version 2.0: 2020-01-22
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description