3B54

Saccharomyces cerevisiae nucleoside diphosphate kinase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure of Ynk1 from the yeast Saccharomyces cerevisiae

Wang, H., Bao, R., Jiang, C., Yang, Z., Zhou, C.-Z., Chen, Y.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 572-576

  • DOI: https://doi.org/10.1107/S1744309108015212
  • Primary Citation of Related Structures:  
    3B54

  • PubMed Abstract: 

    Nucleoside diphosphate kinase (NDPK) catalyzes the transfer of the gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. In addition to biochemical studies, a number of crystal structures of NDPK from various organisms, including both native proteins and complexes with nucleotides or nucleotide analogues, have been determined. Here, the crystal structure of Ynk1, an NDPK from the yeast Saccharomyces cerevisiae, has been solved at 3.1 A resolution. Structural analysis strongly supports the oligomerization state of this protein being hexameric rather than tetrameric.

    • Organizational Affiliation: 

    Protein Research Institute, Tongji University, Shanghai 200092, People's Republic of China.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase
A, B
161Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NDK1, YNK, YNK1
EC: 2.7.4.6
UniProt
Find proteins for P36010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36010 
Go to UniProtKB:  P36010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36010
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.92α = 90
b = 185.92β = 90
c = 185.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description