8ZLA | pdb_00008zla

Crystal Structure of monomeric Rag-like small GTPase from Asgard Lokiarchaeota (LokiRagM) in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb8ZLA/pdb

• Classification: HYDROLASE
• Organism(s): Promethearchaeum syntrophicum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-17 Released: 2025-11-26 
• Deposition Author(s): Alsheikh, F.B., Robinson, R.C.
• Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC), Moore Foundation grant, Simons Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure of monomeric Rag-like small GTPase from Asgard Lokiarchaeota (LokiRagM) in complex with GDP

Alsheikh, F.B., Robinson, R.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.94 kDa 
• Atom Count: 2,942 
• Modeled Residue Count: 319 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein	A	385	Promethearchaeum syntrophicum	Mutation(s): 0  Gene Names: DSAG12_01154
UniProt
Find proteins for A0A5B9D832 (Promethearchaeum syntrophicum) Explore A0A5B9D832  Go to UniProtKB:  A0A5B9D832

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.04	α = 90
b = 85.04	β = 90
c = 153.016	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
DIALS	data reduction
DIALS	data scaling
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Alsheikh, F.B., Robinson, R.C.

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Funding Organization	Location	Grant Number
Vidyasirimedhi Institute of Science and Technology (VISTEC)	Thailand	--
Moore Foundation grant	United Kingdom	GBMF9743
Simons Foundation	United States	GBMF9743

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release