2EGZ | pdb_00002egz

Crystal structure of the 3-dehydroquinate dehydratase from Aquifex aeolicus VF5

• PDB DOI: https://doi.org/10.2210/pdb2EGZ/pdb

• Classification: LYASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-02 Released: 2007-09-04 
• Deposition Author(s): Karthe, P., Kumarevel, T.S., Ebihara, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.237 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Crystal structure of the 3-dehydroquinate dehydratase from Aquifex aeolicus VF5

Karthe, P., Kumarevel, T.S., Ebihara, A., Kuramitsu, S., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.31 kDa 
• Atom Count: 3,585 
• Modeled Residue Count: 434 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B [auth C]	219	Aquifex aeolicus	Mutation(s): 0  Gene Names: aroD EC: 4.2.1.10
UniProt
Find proteins for O66440 (Aquifex aeolicus (strain VF5)) Explore O66440  Go to UniProtKB:  O66440

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	C [auth A], D [auth C]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.237 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.937	α = 90
b = 67.614	β = 99.2
c = 60.238	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Karthe, P., Kumarevel, T.S., Ebihara, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations