3B54 | pdb_00003b54

Saccharomyces cerevisiae nucleoside diphosphate kinase

• PDB DOI: https://doi.org/10.2210/pdb3B54/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-25 Released: 2008-10-07 
• Deposition Author(s): Wang, H.B., Bao, R., Cheng, Y.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.261 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.264 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

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

• PubMed: 18607079 
• DOI: https://doi.org/10.1107/S1744309108015212
• Primary Citation 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.

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Organizational Affiliation: 
• Protein Research Institute, Tongji University, Shanghai 200092, People's Republic of China.

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: 36.61 kDa 
• Atom Count: 2,307 
• Modeled Residue Count: 290 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B	161	Saccharomyces cerevisiae	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.261 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.264 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.92	α = 90
b = 185.92	β = 90
c = 185.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Wang, H.B., Bao, R., Cheng, Y.X.

Revision History  

• 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