5X00 | pdb_00005x00

Nucleoside Diphosphate Kinase from Vibrio cholerae is a Thermolabile Type II tetramer

• PDB DOI: https://doi.org/10.2210/pdb5X00/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae M66-2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-19 Released: 2018-01-31 
• Deposition Author(s): Agnihotri, P., Mishra, A.K., Pratap, J.V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Nucleoside Diphosphate Kinase from Vibrio cholerae is a Thermolabile Type II tetramer.

Agnihotri, P., Mishra, A.K., Pratap, J.V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 32.18 kDa 
• Atom Count: 1,793 
• Modeled Residue Count: 236 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B	144	Vibrio cholerae M66-2	Mutation(s): 0  Gene Names: ndk, VCM66_0714 EC: 2.7.4.6
UniProt
Find proteins for C3LT09 (Vibrio cholerae serotype O1 (strain M66-2)) Explore C3LT09  Go to UniProtKB:  C3LT09

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.37	α = 90
b = 71.21	β = 90
c = 89.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Agnihotri, P., Mishra, A.K., Pratap, J.V.

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description