2CWK

Crystal structure of nucleotide diphosphate kinase from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb2CWK/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-21 Released: 2005-12-21 
• Deposition Author(s): Kato-Murayama, M., Murayama, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.228 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Crystal structure of nucleotide diphosphate kinase from Pyrococcus horikoshii

Kato-Murayama, M., Murayama, K., Shirouzu, M., 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 (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.68 kDa 
• Atom Count: 2,800 
• Modelled Residue Count: 305 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nucleoside-diphosphate kinase	A, B	160	Pyrococcus horikoshii OT3	Mutation(s): 0  EC: 2.7.4.6
UniProt
Find proteins for O58429 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58429  Go to UniProtKB:  O58429

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.228 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.065	α = 90
b = 116.065	β = 90
c = 192.833	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-21 
Deposition Author(s): Kato-Murayama, M., Murayama, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-12-21
  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: 2024-03-13
  Changes: Data collection, Database references