1WYE | pdb_00001wye

Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from Sulfolobus Tokodaii

• PDB DOI: https://doi.org/10.2210/pdb1WYE/pdb

• Classification: TRANSFERASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-12 Released: 2006-07-04 
• Deposition Author(s): Toyoda, T., Suzuki, K., Hossain, M.T., Koike, I., Sekiguchi, T., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.270 (Depositor) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus Tokodaii

Toyoda, T., Suzuki, K., Hossain, M.T., Koike, I., Sekiguchi, T., Takenaka, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 207.14 kDa 
• Atom Count: 14,836 
• Modeled Residue Count: 1,854 
• Deposited Residue Count: 1,866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-keto-3-deoxygluconate kinase	A, B, C, D, E, F	311	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  EC: 2.7.1.45
UniProt
Find proteins for Q96XN9 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96XN9  Go to UniProtKB:  Q96XN9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.270 (Depositor) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.666	α = 90
b = 149.103	β = 90
c = 161.096	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Toyoda, T., Suzuki, K., Hossain, M.T., Koike, I., Sekiguchi, T., Takenaka, A.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2018-06-20
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references