4CL0

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase inhibited by a 3-dehydroquinic acid derivative

• PDB DOI: https://doi.org/10.2210/pdb4CL0/pdb

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


• Deposited: 2014-01-10 Released: 2015-03-25 
• Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Sedes, A., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.228 
• R-Value Work: 0.132 
• R-Value Observed: 0.136 

Starting Model: experimental

Literature

Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase

Maneiro, M., Otero, J.M., Peon, A., Sedes, A., Llamas-Saiz, A.L., Lamb, H., Hawkins, A.R., van Raaij, M.J., Gonzalez-Bello, C.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.88 kDa 
• Atom Count: 1,084 
• Modelled Residue Count: 140 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A	146	Mycobacterium tuberculosis	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9PY	B [auth A]	(2R)-2-METHYL-3-DEHYDROQUINIC ACID C8 H12 O6 YHBCRPWBCJOXAZ-MIZGGHSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.228 
• R-Value Work: 0.132 
• R-Value Observed: 0.136 
• Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.003	α = 90
b = 126.003	β = 90
c = 126.003	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Sedes, A., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description