8YL2 | pdb_00008yl2

Crystal Structure of Homo Tetrameric RagA-like small GTPase from Asgard Lokiarchaeota (LokiRagO) in complex with GTP

PDB DOI: https://doi.org/10.2210/pdb8YL2/pdb

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

Deposited: 2024-03-05 Released: 2025-09-10
Deposition Author(s): Alsheikh, F.B., Robinson, R.C.
Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC), Other private, Simons Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.202 (Depositor), 0.205 (DCC)
R-Value Observed:
0.203 (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

Crystal Structure of Homo Tetrameric RagA-like small GTPase from Asgard Lokiarchaeota (LokiRagO) in complex with GTP

Alsheikh, F.B., Robinson, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 323.7 kDa
Atom Count: 19,749
Modeled Residue Count: 2,315
Deposited Residue Count: 2,736
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein	A, B, C, D, E A, B, C, D, E, F, G, H	342	Promethearchaeum syntrophicum	Mutation(s): 0 Gene Names: DSAG12_02311
UniProt
Find proteins for A0A5B9DBS5 (Promethearchaeum syntrophicum) Explore A0A5B9DBS5 Go to UniProtKB: A0A5B9DBS5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5B9DBS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.202 (Depositor), 0.205 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.756	α = 90
b = 97.183	β = 104.28
c = 145.738	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Alsheikh, F.B.

Robinson, R.C.

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