1V1J

Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro

• PDB DOI: https://doi.org/10.2210/pdb1V1J/pdb

• Classification: LYASE
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-04-16 Released: 2005-01-26 
• Deposition Author(s): Roszak, A.W., Coggins, J.R., Lapthorn, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Starting Model: experimental

Literature

(1R,4S,5R)-3-Fluoro-1,4,5-Trihydroxy-2-Cyclohexene-1-Carboxylic Acid: The Fluoro Analogue of the Enolate Intermediate in the Reaction Catalyzed by Type II Dehydroquinases

Frederickson, M., Roszak, A.W., Coggins, J.R., Lapthorn, A.J., Abell, C.

(2004) Org Biomol Chem 2: 1592

• PubMed: 15162210 
• DOI: https://doi.org/10.1039/b404535a
• Primary Citation of Related Structures:  
  1V1J


• PubMed Abstract: 
  

  The fluoro analogue of the enolate intermediate in the reaction catalyzed by type II dehydroquinases has been prepared from naturally occurring (-)-quinic acid over seven steps and has been shown to be the most potent inhibitor reported to date of the type II enzyme from Mycobacterium tuberculosis.

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Organizational Affiliation: 

University Chemical Laboratory, Lensfield Road, Cambridge, UK CB2 1EW.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 203.2 kDa 
• Atom Count: 14,496 
• Modelled Residue Count: 1,800 
• Deposited Residue Count: 1,884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C, D, E, F, G, H, I, J, K, L	157	Streptomyces coelicolor	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore P15474  Go to UniProtKB:  P15474

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FA3	BA [auth L], M [auth A], O [auth B], P [auth C], Q [auth D], R [auth E], T [auth F], U [auth G], V [auth H], W [auth I], Y [auth J], Z [auth K]	2-ANHYDRO-3-FLUORO-QUINIC ACID C7 H9 F O5 DGZQZSSRYAJDAX-XAHCXIQSSA-N
TRS	AA [auth K], N [auth A], S [auth E], X [auth I]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
FA3	PDBBind:  1V1J	Ki: 1.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.475	α = 90
b = 138.941	β = 90
c = 141.925	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-26 
Deposition Author(s): Roszak, A.W., Coggins, J.R., Lapthorn, A.J.

Revision History  

• Version 1.0: 2005-01-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description