8B3S | pdb_00008b3s

Structure of YjbA in complex with ClpC N-terminal Domain

• PDB DOI: https://doi.org/10.2210/pdb8B3S/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-16 Released: 2023-12-27 
• Deposition Author(s): Evans, N.J., Isaacson, R.L., Camp, A.H., Collins, M.K.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structure of YjbA in complex with ClpC N-terminal Domain

Evans, N.J., Isaacson, R.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, isothermal titration calorimetry, assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 59.89 kDa 
• Atom Count: 3,426 
• Modeled Residue Count: 387 
• Deposited Residue Count: 507 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0736 protein B4122_0676,UPF0736 protein YjbA	A	351	Bacillus subtilis	Mutation(s): 0  Gene Names: B4122_0676, B4417_4067, Bateq7PJ16_1268, DFO69_2911, J5227_16610, SC09_Contig19orf00439, yjbA, BSU11410
UniProt
Find proteins for O31597 (Bacillus subtilis (strain 168)) Explore O31597  Go to UniProtKB:  O31597

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpC / Negative regulator of tic competence clcC/mecB	B [auth Z]	156	Bacillus subtilis	Mutation(s): 0  Gene Names: B4417_1475
UniProt
Find proteins for P37571 (Bacillus subtilis (strain 168)) Explore P37571  Go to UniProtKB:  P37571

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth Z], H [auth Z]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	I [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.713	α = 90
b = 69.713	β = 90
c = 89.601	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing
SHELXDE	phasing
ARP/wARP	model building
BUCCANEER	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Evans, N.J., Isaacson, R.L., Camp, A.H., Collins, M.K.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary