8PRC

The structure of v13Bagel8

• PDB DOI: https://doi.org/10.2210/pdb8PRC/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Dictyoglomus thermophilum H-6-12
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-07-12 Released: 2024-07-24 
• Deposition Author(s): Vandebroek, L., Voet, A.R.D., Lee, X.Y.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.312 
• R-Value Work: 0.238 
• R-Value Observed: 0.242 

Literature

The structure of v13Bagel8

Vandebroek, L., Voet, A.R.D., Lee, X.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 9.3 kDa 
• Atom Count: 628 
• Modelled Residue Count: 80 
• Deposited Residue Count: 85 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell surface protein	A	85	Dictyoglomus thermophilum H-6-12	Mutation(s): 0  Gene Names: DICTH_0179
UniProt
Find proteins for B5YBJ6 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12)) Explore B5YBJ6  Go to UniProtKB:  B5YBJ6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.312 
• R-Value Work: 0.238 
• R-Value Observed: 0.242 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.159	α = 90
b = 54.159	β = 90
c = 109.537	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Vandebroek, L., Voet, A.R.D., Lee, X.Y.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1235722N

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release