4V0S

Crystal structure of Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant inhibited by a 3-dehydroquinic acid derivative

• PDB DOI: https://doi.org/10.2210/pdb4V0S/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2014-09-18 Released: 2016-01-13 
• Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Santiago, C., Lamb, H., Hawkins, A.R., Maneiro, M., Peon, A., Gonzalez-Bello, C., van Raaij, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.189 
• R-Value Work: 0.135 
• R-Value Observed: 0.138 

Starting Model: experimental

Literature

Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase

Maneiro, M., Otero, J.M., Peon, A., van Raaij, M.J., Lamb, H., Hawkings, A.R., Gonzalez-Bello, C.

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: 32.89 kDa 
• Atom Count: 2,423 
• Modelled Residue Count: 283 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B	146	Mycobacterium tuberculosis	Mutation(s): 1  EC: 4.2.1.10
UniProt
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX7  Go to UniProtKB:  P9WPX7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2HN	C [auth A], D [auth A], H [auth B]	(1R,2S,4S,5R)-2-(2,3,4,5,6-pentafluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid C14 H11 F5 O6 ZNZHQTVBMHBUCF-GLOYCNQYSA-N
7HN	E [auth A]	3,4-DIHYDROXY-2-[(2,3,4,5,6-PENTAFLUOROPHENYL)METHYL]BENZOIC ACID C14 H7 F5 O4 OKFLUGFRGVSRHK-UHFFFAOYSA-N
CL	F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.189 
• R-Value Work: 0.135 
• R-Value Observed: 0.138 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.848	α = 90
b = 65.187	β = 90
c = 94.755	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Santiago, C., Lamb, H., Hawkins, A.R., Maneiro, M., Peon, A., Gonzalez-Bello, C., van Raaij, M.J.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description