1SFJ

2.4A Crystal structure of Staphylococcus aureus type I 3-dehydroquinase, with 3-dehydroquinate bound

• PDB DOI: https://doi.org/10.2210/pdb1SFJ/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus MRSA252
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-02-19 Released: 2004-10-12 
• Deposition Author(s): Nichols, C.E., Lockyer, M., Hawkins, A.R., Stammers, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.250 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Crystal structures of Staphylococcus aureus type I dehydroquinase from enzyme turnover experiments

Nichols, C.E., Lockyer, M., Hawkins, A.R., Stammers, D.K.

(2004) Proteins 56: 625-628

• PubMed: 15229896 
• DOI: https://doi.org/10.1002/prot.20165
• Primary Citation of Related Structures:  
  1SFJ, 1SFL

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Organizational Affiliation: 

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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: 54.51 kDa 
• Atom Count: 3,957 
• Modelled Residue Count: 460 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B	238	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0  Gene Names: aroD EC: 4.2.1.10
UniProt
Find proteins for Q6GII7 (Staphylococcus aureus (strain MRSA252)) Explore Q6GII7  Go to UniProtKB:  Q6GII7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHK	C [auth A], D [auth B]	3-DEHYDROSHIKIMATE C7 H10 O5 YVYKOQWMJZXRRM-UYFOZJQFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.250 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.58	α = 90
b = 76.58	β = 90
c = 172.44	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-12 
Deposition Author(s): Nichols, C.E., Lockyer, M., Hawkins, A.R., Stammers, D.K.

Revision History  

• Version 1.0: 2004-10-12
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary