2DEJ | pdb_00002dej

Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PN and galactose

• PDB DOI: https://doi.org/10.2210/pdb2DEJ/pdb

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


• Deposited: 2006-02-10 Released: 2007-05-01 
• Deposition Author(s): Inagaki, E., Sakamoto, K., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of galaktokinase from Pyrococcus horikoshii

Inagaki, E., Sakamoto, K., Shinkai, A., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.03 kDa 
• Atom Count: 3,158 
• Modeled Residue Count: 346 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable galactokinase	A	350	Pyrococcus horikoshii	Mutation(s): 0  EC: 2.7.1.6
UniProt
Find proteins for O58107 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58107  Go to UniProtKB:  O58107

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APW	C [auth A]	{5'-O-[(R)-{[(S)-AMINO(HYDROXY-KAPPAO)PHOSPHORYL]OXY}(HYDROXY-KAPPAO)PHOSPHORYL]ADENOSINATO(2-)}MAGNESIUM C10 H14 Mg N6 O9 P2 XFWUVFOBMRZZRT-MCDZGGTQSA-L
GLA	B [auth A]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.945	α = 90
b = 38.997	β = 109.6
c = 81.188	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BSS	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Inagaki, E., Sakamoto, K., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary