2O7S | pdb_00002o7s

Crystal Structure of the A. thaliana DHQ-dehydroshikimate-SDH-shikimate-NADP(H)

• PDB DOI: https://doi.org/10.2210/pdb2O7S/pdb

• Classification: OXIDOREDUCTASE, TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-11 Released: 2007-11-20 
• Deposition Author(s): Christendat, D., Singh, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.233 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.227 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Literature

The DHQ-dehydroshikimate-SDH-shikimate-NADP(H) Complex: Insights into Metabolite Transfer in the Shikimate Pathway

Singh, S.A., Christendat, D.

(2007) Cryst Growth Des 7: 2153-2160

• DOI: https://doi.org/10.1021/cg7007107

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.46 kDa 
• Atom Count: 4,150 
• Modeled Residue Count: 500 
• Deposited Residue Count: 523 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase	A	523	Arabidopsis thaliana	Mutation(s): 2  Gene Names: EMB3004 EC: 1.1.1.25 (PDB Primary Data), 4.2.1.10 (PDB Primary Data)
UniProt
Find proteins for Q9SQT8 (Arabidopsis thaliana) Explore Q9SQT8  Go to UniProtKB:  Q9SQT8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	F [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
DHK	C [auth A], E [auth A]	3-DEHYDROSHIKIMATE C7 H10 O5 YVYKOQWMJZXRRM-UYFOZJQFSA-N
TLA	D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.233 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.227 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.447	α = 90
b = 97.447	β = 90
c = 116.43	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
CNS	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Christendat, D., Singh, S.A.

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-11-20
  Changes: Structure summary