2UYG | pdb_00002uyg

Crystallogaphic structure of the typeII 3-Dehydroquinase from Thermus Thermophilus

• PDB DOI: https://doi.org/10.2210/pdb2UYG/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2007-04-05 Released: 2008-05-27 
• Deposition Author(s): Utsunomiya, H., Agari, Y., Imagawa, T., Tsuge, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.277 (Depositor) 
• R-Value Work: 
  0.230 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Crystallogaphic Structure of the Typeii 3-Dehydroquinase from Thermus Thermophilus

Utsunomiya, H., Agari, Y., Imagawa, T., Tsuge, H.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 198.73 kDa 
• Atom Count: 13,475 
• Modeled Residue Count: 1,704 
• Deposited Residue Count: 1,788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C, D, E, F, G, H, I, J, K, L	149	Thermus thermophilus HB8	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for Q5SIL5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIL5  Go to UniProtKB:  Q5SIL5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.277 (Depositor) 
• R-Value Work:  0.230 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.085	α = 90
b = 151.586	β = 90
c = 159.949	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Utsunomiya, H., Agari, Y., Imagawa, T., Tsuge, H.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-04-10
  Changes: Data collection, Other, Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description