6AES | pdb_00006aes

Crystal structure of Nucleoside diphosphate kinase from Pseudomonas aeruginosa at 3.55 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb6AES/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-06 Released: 2018-09-12 
• Deposition Author(s): Sikarwar, J., Singh, P.K., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 
  0.332 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.286 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.289 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Nucleoside diphosphate kinase from Pseudomonas aeruginosa at 3.55 A resolution.

Sikarwar, J., Singh, P.K., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 124.9 kDa 
• Atom Count: 8,759 
• Modeled Residue Count: 1,144 
• Deposited Residue Count: 1,144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B, C, D, E, F, G, H	143	Pseudomonas aeruginosa	Mutation(s): 0  EC: 2.7.4.6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free:  0.332 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.286 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.289 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.566	α = 99.6
b = 70.875	β = 109.12
c = 71.097	γ = 90.25

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Sikarwar, J., Singh, P.K., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description