1J2Y

Crystal structure of the type II 3-dehydroquinase

• PDB DOI: https://doi.org/10.2210/pdb1J2Y/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-15 Released: 2003-06-24 
• Deposition Author(s): Lee, B.I., Kwak, J.E., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Crystal structure of the type II 3-dehydroquinase from Helicobacter pylori

Lee, B.I., Kwak, J.E., Suh, S.W.

(2003) Proteins 51: 616-617

• PubMed: 12784220 
• DOI: https://doi.org/10.1002/prot.10415
• Primary Citation of Related Structures:  
  1J2Y

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Organizational Affiliation: 

Laboratory of Structural Proteomics, School of Chemistry and Molecular Engineering, Seoul National University, Seoul, Korea.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 18.69 kDa 
• Atom Count: 1,253 
• Modelled Residue Count: 158 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A	167	Helicobacter pylori	Mutation(s): 0  Gene Names: aroQ EC: 4.2.1.10
UniProt
Find proteins for Q48255 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore Q48255  Go to UniProtKB:  Q48255

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DQA	B [auth A]	1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID C7 H10 O6 WVMWZWGZRAXUBK-SYTVJDICSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 4₂ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.91	α = 90
b = 98.91	β = 90
c = 98.91	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-24 
Deposition Author(s): Lee, B.I., Kwak, J.E., Suh, S.W.

Revision History  

• Version 1.0: 2003-06-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description