8PRA

The structure of v13Bagel4

• PDB DOI: https://doi.org/10.2210/pdb8PRA/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): synthetic construct
• 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: 2.05 Å
• R-Value Free: 0.312 
• R-Value Work: 0.274 
• R-Value Observed: 0.276 

Literature

The structure of v13Bagel4

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

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.91 kDa 
• Atom Count: 4,988 
• Modelled Residue Count: 640 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell surface protein	A, B, C, D	165	synthetic construct	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.312 
• R-Value Work: 0.274 
• R-Value Observed: 0.276 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.708	α = 90
b = 83.499	β = 90
c = 97.684	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
DIALS	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