3EWM

Crystal structure of an uncharacterized sugar kinase PH1459 from pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb3EWM/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-15 Released: 2008-11-18 
• Deposition Author(s): Kumar, G., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.239 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Crystal structure of an uncharacterized sugar kinase PH1459 from pyrococcus horikoshii

Kumar, G., Eswaramoorthy, S., Burley, S.K., Swaminathan, 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 (software)

Macromolecule Content

• Total Structure Weight: 69.53 kDa 
• Atom Count: 5,025 
• Modelled Residue Count: 595 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized sugar kinase PH1459	A, B	313	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH1459, PHCC008 EC: 2.7.1
UniProt
Find proteins for O59128 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59128  Go to UniProtKB:  O59128

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.239 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.757	α = 90
b = 79.373	β = 94.18
c = 82.99	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-18 
Deposition Author(s): Kumar, G., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references