8OGH

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis with butylacetylphosphonate (BAP) bound

• PDB DOI: https://doi.org/10.2210/pdb8OGH/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-20 Released: 2023-05-10 
• Deposition Author(s): Gawriljuk, O.V., Oerlemans, R., Groves, R.M.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.172 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Literature

Structure of Mycobacterium tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Synthase in Complex with Butylacetylphosphonate

Gawriljuk, V.O., Oerlemans, R., Gierse, R.M., Jotwani, R., Hirsch, A.K.H., Groves, M.R.

(2023) Crystals (Basel) 13

• DOI: https://doi.org/10.3390/cryst13050737

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 129.45 kDa 
• Atom Count: 9,915 
• Modelled Residue Count: 1,097 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose-5-phosphate synthase	A, B	604	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: dxs, Rv2682c, MTCY05A6.03c EC: 2.2.1.7
UniProt
Find proteins for P9WNS3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNS3  Go to UniProtKB:  P9WNS3

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VMI (Subject of Investigation/LOI)	C [auth A], M [auth B]	[(S)-1-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1-oxidanyl-ethyl]-butoxy-phosphinic acid C18 H32 N4 O11 P3 S KQPODQFTFSEDTF-SFHVURJKSA-O
PEG	Q [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	L [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.172 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.462	α = 90
b = 127.775	β = 106.883
c = 79.583	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Gawriljuk, O.V., Oerlemans, R., Groves, R.M.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	860816

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 2.0: 2023-10-25
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary