7YH1

Roadblock from Candidatus Prometheoarchaeum syntrophicum strain MK-D1

• PDB DOI: https://doi.org/10.2210/pdb7YH1/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Candidatus Prometheoarchaeum syntrophicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-12 Released: 2023-07-19 
• Deposition Author(s): Robinson, R.C., Tran, L.T.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Literature

Roadblock from Candidatus Prometheoarchaeum syntrophicum strain MK-D1

Robinson, R.C., Tran, L.T.

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 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)

Macromolecule Content

• Total Structure Weight: 52.3 kDa 
• Atom Count: 3,686 
• Modelled Residue Count: 464 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Roadblock/LC7 domain protein	A [auth D], B [auth A], C [auth B], D [auth C]	117	Candidatus Prometheoarchaeum syntrophicum	Mutation(s): 0  Gene Names: DSAG12_02202
UniProt
Find proteins for A0A5B9DB95 (Candidatus Prometheoarchaeum syntrophicum) Explore A0A5B9DB95  Go to UniProtKB:  A0A5B9DB95

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth D], F [auth D], G [auth D], H [auth D], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth C], P [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.338	α = 76.65
b = 53.574	β = 75.32
c = 59.856	γ = 80.61

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Robinson, R.C., Tran, L.T.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR19S5
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H00476
Other private		Moore and Simons foundations GBMF9743

Revision History  

• Version 1.0: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description