1SG6

Crystal structure of Aspergillus nidulans 3-dehydroquinate synthase (AnDHQS) in complex with Zn2+ and NAD+, at 1.7D

• PDB DOI: https://doi.org/10.2210/pdb1SG6/pdb

• Classification: LYASE
• Organism(s): Aspergillus nidulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-02-23 Released: 2004-08-31 
• Deposition Author(s): Nichols, C.E., Hawkins, A.R., Stammers, D.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.250 
• R-Value Work: 0.195 
• R-Value Observed: 0.250 

Starting Model: experimental

Literature

Structure of the 'open' form of Aspergillus nidulans 3-dehydroquinate synthase at 1.7 A resolution from crystals grown following enzyme turnover.

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

(2004) Acta Crystallogr D Biol Crystallogr 60: 971-973

• PubMed: 15103156 
• DOI: https://doi.org/10.1107/S0907444904004743
• Primary Citation of Related Structures:  
  1SG6


• PubMed Abstract: 
  

  Crystallization of Aspergillus nidulans 3-dehydroquinate synthase (DHQS), following turnover of the enzyme by addition of the substrate DAHP, gave a new crystal form (form J). Although the crystals have dimensions of only 50 x 20 x 5 micro m, they are well ordered, diffracting to 1.7 A. The space group is C222(1), with unit-cell parameters a = 90.0, b = 103.7, c = 177.4 A. Structure determination and refinement to R = 0.19 (R(free) = 0.25) shows the DHQS is in the 'open' form with the substrate site unoccupied but with some loop regions perturbed. Previous crystals of open-form DHQS only diffracted to 2.5 A resolution. The use of enzyme turnover may be applicable in other systems in attempts to improve crystal quality.

---

Organizational Affiliation: 

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.39 kDa 
• Atom Count: 7,181 
• Modelled Residue Count: 755 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentafunctional AROM polypeptide	A, B	393	Aspergillus nidulans	Mutation(s): 0  Gene Names: AROMA, AROM EC: 4.2.3.4
UniProt
Find proteins for P07547 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore P07547  Go to UniProtKB:  P07547

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.250 
• R-Value Work: 0.195 
• R-Value Observed: 0.250 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.02	α = 90
b = 104.51	β = 90
c = 177.44	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: 2004-08-31 
Deposition Author(s): Nichols, C.E., Hawkins, A.R., Stammers, D.K.

Revision History  

• Version 1.0: 2004-08-31
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description