6H5D

Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 2

• PDB DOI: https://doi.org/10.2210/pdb6H5D/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-24 Released: 2019-07-24 
• Deposition Author(s): Sanz-Gaitero, M., Maneiro, M., Lence, E., Otero, J.M., Thompson, P., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.200 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Hydroxylammonium Derivatives for Selective Active-site Lysine Modification in the Anti-virulence Bacterial Target DHQ1 Enzyme.

Maneiro, M., Lence, E., Sanz-Gaitero, M., Otero, J.M., van Raaij, M.J., Thompson, P., Hawkins, A.R., Gonzalez-Bello, C.

(2019) Org Chem Front 9: 3127-3135

• DOI: https://doi.org/10.1039/c9qo00453j

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: 55.74 kDa 
• Atom Count: 4,841 
• Modelled Residue Count: 504 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B	252	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  Gene Names: aroD, STY1760, t1231 EC: 4.2.1.10
UniProt
Find proteins for P24670 (Salmonella typhi) Explore P24670  Go to UniProtKB:  P24670

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WPL (Subject of Investigation/LOI)	C [auth A], D [auth B]	(1~{S},3~{S},4~{R},5~{R})-3-methyl-1,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid C8 H14 O5 NMVUNDOHFYILSF-FJDLHZNMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.200 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.219	α = 90
b = 44.057	β = 95.25
c = 84.6	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Sanz-Gaitero, M., Maneiro, M., Lence, E., Otero, J.M., Thompson, P., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	BFU2014-53425-P

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2019-08-28
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2019-10-09
  Changes: Data collection, Database references
• Version 1.4: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary