4W98 | pdb_00004w98

Acinetobacter baumannii SDF NDK

• PDB DOI: https://doi.org/10.2210/pdb4W98/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii SDF
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-27 Released: 2015-06-17 
• Deposition Author(s): Hu, Y., Feng, F., Liang, H., Liu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Characterization of Acinetobacter baumannii Nucleoside Diphosphate Kinase

Hu, Y., Feng, F., Liu, Y.

(2015) PROG BIOCHEM BIOPHYS 42: 260-267

• DOI: https://doi.org/10.16476/j.pibb.2014.0319

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 15.76 kDa 
• Atom Count: 1,276 
• Modeled Residue Count: 145 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A	145	Acinetobacter baumannii SDF	Mutation(s): 0  Gene Names: ndk, ABSDF3006 EC: 2.7.4.6
UniProt
Find proteins for B0VKS3 (Acinetobacter baumannii (strain SDF)) Explore B0VKS3  Go to UniProtKB:  B0VKS3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.726	α = 90
b = 76.962	β = 90
c = 82.239	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Hu, Y., Feng, F., Liang, H., Liu, Y.

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy