7EWS | pdb_00007ews

Crystal structure of arginine kinase (AK3) from the ciliate Paramecium tetraurelia

• PDB DOI: https://doi.org/10.2210/pdb7EWS/pdb

• Classification: TRANSFERASE
• Organism(s): Paramecium tetraurelia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-26 Released: 2022-06-01 
• Deposition Author(s): Otsuka, Y., Yokota, J., Yano, D., Uda, K., Suzuki, T., Sugiyama, S.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of arginine kinase (AK3) from the ciliate Paramecium tetraurelia

Otsuka, Y., Yokota, J., Yano, D., Uda, K., Suzuki, T., Sugiyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 91.05 kDa 
• Atom Count: 6,761 
• Modeled Residue Count: 756 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
arginine kinase	A, B	401	Paramecium tetraurelia	Mutation(s): 0
UniProt
Find proteins for A0C7I4 (Paramecium tetraurelia) Explore A0C7I4  Go to UniProtKB:  A0C7I4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.109	α = 90
b = 77.727	β = 90
c = 162.197	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Otsuka, Y., Yokota, J., Yano, D., Uda, K., Suzuki, T., Sugiyama, S.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJTM19DC
Japan Society for the Promotion of Science (JSPS)	Japan	19K06588
Other private	Japan	09-003-005

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description