8BJV

Crystal structure of YopR

• PDB DOI: https://doi.org/10.2210/pdb8BJV/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-08 Released: 2023-11-22 
• Deposition Author(s): Gallego del Sol, F., Marina, A.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 

Literature

Crystal structure of YopR from SPbeta phage

Gallego del Sol, F., Marina, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 113.18 kDa 
• Atom Count: 8,073 
• Modelled Residue Count: 963 
• Deposited Residue Count: 978 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPbeta prophage-derived uncharacterized protein YopR	A, B, C	326	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: yopR, BSU20790
UniProt
Find proteins for O34558 (Bacillus subtilis (strain 168)) Explore O34558  Go to UniProtKB:  O34558

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth B], F [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.912	α = 90
b = 107.75	β = 90.8
c = 52.87	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Gallego del Sol, F., Marina, A.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	--

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release