8YV4 | pdb_00008yv4

The crystal structure of G.acetivorans RNA kinase Ark1

PDB DOI: https://doi.org/10.2210/pdb8YV4/pdb

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

Deposited: 2024-03-27 Released: 2025-04-02
Deposition Author(s): Cao, C.L., Gan, J.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of G.acetivorans RNA kinase Ark1

Cao, C.L., Gan, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 42 kDa
Atom Count: 2,924
Modeled Residue Count: 342
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative serine/threonine protein kinase	A, B	174	Geoglobus acetivorans	Mutation(s): 0 Gene Names: GACE_0057
UniProt
Find proteins for A0A0A7GDU7 (Geoglobus acetivorans) Explore A0A0A7GDU7 Go to UniProtKB: A0A0A7GDU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A7GDU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.87	α = 90
b = 63.297	β = 109.46
c = 70.22	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.