Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.88 kDa 
• Atom Count: 1060 
• Modelled Residue Count: 149 
• Deposited Residue Count: 150 
• Unique protein chains: 1

1NB2

Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans

• PDB DOI: 10.2210/pdb1NB2/pdb

• Classification: TRANSFERASE
• Organism(s): Virgibacillus halodenitrificans
• Mutation(s): No 


• Deposited: 2002-12-02 Released: 2003-05-06 
• Deposition Author(s): Chen, C.-J., Liu, M.-Y., Chang, W.-C., Chang, T., Wang, B.-C., Le Gall, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.213 
• R-Value Observed: 0.229 

Literature

Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase.

Chen, C.-J., Liu, M.-Y., Chang, T., Chang, W.-C., Wang, B.-C., Le Gall, J.

(2003) J Struct Biol 142: 247-255

• PubMed: 12713952 
• DOI: 10.1016/s1047-8477(03)00014-5
• Primary Citation of Related Structures:  
  1NB2


• PubMed Abstract: 
  

We found that when grown under anaerobic conditions the moderate halophile, gram-positive bacterium Bacillus halodenitrificans (ATCC 49067) synthesizes large amounts of a polypeptide complex that contains a heme center capable of reversibly bind nitric oxide. This complex, when exposed to air, dissociates and reassociates into two active components, a Mn-containing superoxide dismutase (SOD) and a nucleoside diphosphate kinase (BhNDK). The crystal structure of this latter enzyme has been determined at 2.2A resolution using molecular replacement method, based on the crystal structure of Drosophila melanogaster NDK. The model contains 149 residues of a total 150 residues and 34 water molecules. BhNDK consists of a four-stranded antiparallel beta-sheet, whose surfaces are partially covered by six alpha-helices, and its overall and active site structures are similar to those of homologous enzymes. However, the hexameric packing of BhNDK shows that this enzyme is different from both eukaryotic and gram-negative bacteria. The need for the bacterium to presynthesize both SOD and NDK precursors which are activated during the anaerobic-aerobic transition is discussed.

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Organizational Affiliation: 

X-ray Structural Biology Group, National Synchrotron Radiation Research Center, Hsinchu 30077, Taiwan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside Diphosphate Kinase	A	150	Virgibacillus halodenitrificans	Mutation(s): 0  Gene Names: ndk EC: 2.7.4.6
UniProt
Find proteins for Q7SIA9 (Virgibacillus halodenitrificans) Explore Q7SIA9  Go to UniProtKB:  Q7SIA9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.213 
• R-Value Observed: 0.229 
• Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.07	α = 90
b = 114.07	β = 90
c = 114.07	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-02 
• Released Date: 2003-05-06 
Deposition Author(s): Chen, C.-J., Liu, M.-Y., Chang, W.-C., Chang, T., Wang, B.-C., Le Gall, J.

Revision History  

• Version 1.0: 2003-05-06
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance