1QD9

Bacillus subtilis YABJ

• PDB DOI: https://doi.org/10.2210/pdb1QD9/pdb

• Classification: GENE REGULATION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-07-09 Released: 1999-11-26 
• Deposition Author(s): Smith, J.L., Sinha, S., Rappu, P., Lange, S.C., Mantsala, P., Zalkin, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.197 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 

Literature

Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family.

Sinha, S., Rappu, P., Lange, S.C., Mantsala, P., Zalkin, H., Smith, J.L.

(1999) Proc Natl Acad Sci U S A 96: 13074-13079

• PubMed: 10557275 
• DOI: https://doi.org/10.1073/pnas.96.23.13074
• Primary Citation of Related Structures:  
  1QD9


• PubMed Abstract: 
  

  The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-A crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c/YjgF/UK114 family of proteins.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 41.63 kDa 
• Atom Count: 3,383 
• Modelled Residue Count: 372 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PURINE REGULATORY PROTEIN YABJ	A, B, C	124	Bacillus subtilis	Mutation(s): 0  EC: 3.5.99.10
UniProt
Find proteins for P37552 (Bacillus subtilis (strain 168)) Explore P37552  Go to UniProtKB:  P37552

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EMC	G [auth B], K [auth C]	ETHYL MERCURY ION C2 H5 Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N
HG	D [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ACY	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.197 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.35	α = 90
b = 53.35	β = 90
c = 204.96	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-26 
Deposition Author(s): Smith, J.L., Sinha, S., Rappu, P., Lange, S.C., Mantsala, P., Zalkin, H.

Revision History  

• Version 1.0: 1999-11-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations