9JUE | pdb_00009jue

Roadblock3 homodimer structure from Candidatus Prometheoarchaeum syntrophicum strain MK-D1

• PDB DOI: https://doi.org/10.2210/pdb9JUE/pdb

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


• Deposited: 2024-10-08 Released: 2024-10-16 
• Deposition Author(s): Ponlachantra, K., Robinson, R.C.
• Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC), Simons Foundation, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: in silico

Literature

Roadblock domain protein from Asgard archaea

Ponlachantra, K., Robinson, R.C.

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: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 84.55 kDa 
• Atom Count: 5,571 
• Modeled Residue Count: 718 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Roadblock/LC7 domain protein	A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	131	Promethearchaeum syntrophicum	Mutation(s): 0  Gene Names: DSAG12_02037
UniProt
Find proteins for A0A5B9DBI1 (Promethearchaeum syntrophicum) Explore A0A5B9DBI1  Go to UniProtKB:  A0A5B9DBI1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE (Subject of Investigation/LOI)	G [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.692	α = 90
b = 88.909	β = 90
c = 112.416	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Ponlachantra, K., Robinson, R.C.

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

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release