8YQG | pdb_00008yqg

Dimeric structure of the Longin domain from a Lokiarchaeota archaeon Roadblock-Longin protein

PDB DOI: https://doi.org/10.2210/pdb8YQG/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Promethearchaeum syntrophicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-19 Released: 2025-03-26
Deposition Author(s): Kitaoku, Y., Sitthisak, P., Robinson, R.C.
Funding Organization(s): Simons Foundation, Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.190 (Depositor), 0.189 (DCC)
R-Value Observed:
0.192 (Depositor)

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

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

Literature

Structure of the Longin domain from a Lokiarchaeota archaeon Roadblock-Longin protein

Sitthisak, P., Kitaoku, Y., Robinson, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 37.66 kDa
Atom Count: 2,800
Modeled Residue Count: 311
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Longin domain	A, B	161	Promethearchaeum syntrophicum	Mutation(s): 0 Gene Names: DSAG12_01965
UniProt
Find proteins for A0A5B9DBT7 (Promethearchaeum syntrophicum) Explore A0A5B9DBT7 Go to UniProtKB: A0A5B9DBT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5B9DBT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.190 (Depositor), 0.189 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.233	α = 90
b = 120.758	β = 104.31
c = 44.807	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Simons Foundation	United States	GBMF9743
Japan Science and Technology	Japan	PMJCR19S5

Revision History (Full details and data files)

Version 1.0: 2025-03-26
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.