2YSW | pdb_00002ysw

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

• PDB DOI: https://doi.org/10.2210/pdb2YSW/pdb

• Classification: LYASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-04 Released: 2007-10-09 
• Deposition Author(s): Tanaka, T., Kumarevel, T.S., Ebihara, A., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

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

Kumarevel, T.S., Tanaka, T., Kuramitsu, S., Yokoyama, S.

To be published.

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,PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 75.01 kDa 
• Atom Count: 5,508 
• Modeled Residue Count: 657 
• Deposited Residue Count: 657 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.796	α = 90
b = 131.796	β = 90
c = 108.012	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Tanaka, T., Kumarevel, T.S., Ebihara, A., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary