8YV5 | pdb_00008yv5

The crystal structure of G. acetivorans RNA kinase Ark1 in complex with ATP

• PDB DOI: https://doi.org/10.2210/pdb8YV5/pdb

• Classification: TRANSFERASE
• Organism(s): Geoglobus acetivorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-28 Released: 2025-04-02 
• Deposition Author(s): Cao, C.L., Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

Literature

The crystal structure of G.acetivorans RNA kinase Ark1

Cao, C.L., Gan, J.H.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.4 kDa 
• Atom Count: 3,091 
• Modeled Residue Count: 345 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative serine/threonine protein kinase	A [auth B], B [auth A]	175	Geoglobus acetivorans	Mutation(s): 0  Gene Names: GACE_0057
UniProt
Find proteins for A0A0A7GDU7 (Geoglobus acetivorans) Explore A0A0A7GDU7  Go to UniProtKB:  A0A0A7GDU7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	D [auth B], G [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL (Subject of Investigation/LOI)	C [auth B], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.92	α = 90
b = 146.92	β = 90
c = 146.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Cao, C.L., Gan, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release