2AZ1

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum

• PDB DOI: https://doi.org/10.2210/pdb2AZ1/pdb

• Classification: TRANSFERASE
• Organism(s): Halobacterium salinarum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-09 Released: 2005-12-20 
• Deposition Author(s): Besir, H., Zeth, K., Bracher, A., Heider, U., Ishibashi, M., Tokunaga, M., Oesterhelt, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.289 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum

Besir, H., Zeth, K., Bracher, A., Heider, U., Ishibashi, M., Tokunaga, M., Oesterhelt, D.

(2005) FEBS Lett 579: 6595-6600

• PubMed: 16293253 
• DOI: https://doi.org/10.1016/j.febslet.2005.10.052
• Primary Citation of Related Structures:  
  2AZ1, 2AZ3


• PubMed Abstract: 
  

  Nucleoside diphosphate kinase from the halophilic archaeon Halobacterium salinarum was crystallized in a free state and a substrate-bound form with CDP. The structures were solved to a resolution of 2.35 and 2.2A, respectively. Crystals with the apo-form were obtained with His6-tagged enzyme, whereas the untagged form was used for co-crystallization with the nucleotide. Crosslinking under different salt and pH conditions revealed a stronger oligomerization tendency for the tagged protein at low and high salt concentrations. The influence of the His6-tag on the halophilic nature of the enzyme is discussed on the basis of the observed structural properties.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Abteilung Membranbiochemie, Am Klopferspitz 18, 82152 Martinsried, Germany. [e-mail]

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: 121.75 kDa 
• Atom Count: 7,204 
• Modelled Residue Count: 921 
• Deposited Residue Count: 1,086 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B, C, D, E, F	181	Halobacterium salinarum	Mutation(s): 0  EC: 2.7.4.6
UniProt
Find proteins for P61136 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P61136  Go to UniProtKB:  P61136

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	G [auth A], H [auth C], I [auth C], J [auth D], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.289 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.28	α = 90
b = 108.7	β = 90
c = 119.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-20 
Deposition Author(s): Besir, H., Zeth, K., Bracher, A., Heider, U., Ishibashi, M., Tokunaga, M., Oesterhelt, D.

Revision History  

• Version 1.0: 2005-12-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description