3JS9

Crystal structure of nucleoside diphosphate kinase family protein from Babesia bovis

• PDB DOI:  https://doi.org/10.2210/pdb3JS9/pdb

• Classification: TRANSFERASE
• Organism(s): Babesia bovis T2Bo
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-09 Released: 2009-09-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Crystal structure of nucleoside diphosphate kinase family protein from Babesia bovis

Edwards, T.E., Staker, B.L., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.39 kDa 
• Atom Count: 3,728 
• Modelled Residue Count: 444 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase family protein	A, B, C	156	Babesia bovis T2Bo	Mutation(s): 0  Gene Names: BBOV_III005290
UniProt
Find proteins for A7ANF8 (Babesia bovis) Explore A7ANF8  Go to UniProtKB:  A7ANF8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33JS9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.894	α = 90
b = 125.894	β = 90
c = 101.512	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description