3ZZQ

Engineered 12-subunit Bacillus subtilis trp RNA-binding attenuation protein (TRAP)

• PDB DOI: https://doi.org/10.2210/pdb3ZZQ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-09-02 Released: 2011-10-12 
• Deposition Author(s): Chen, C., Smits, C., Dodson, G.G., Shevtsov, M.B., Merlino, N., Gollnick, P., Antson, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 

Literature

How to Change the Oligomeric State of a Circular Protein Assembly: Switch from 11-Subunit to 12-Subunit Trap Suggests a General Mechanism

Chen, C., Smits, C., Dodson, G.G., Shevtsov, M.B., Merlino, N., Gollnick, P., Antson, A.A.

(2011) PLoS One 6: 25296

• PubMed: 21984911 
• DOI: https://doi.org/10.1371/journal.pone.0025296
• Primary Citation of Related Structures:  
  3ZZL, 3ZZQ, 3ZZS


• PubMed Abstract: 
  

  Many critical cellular functions are performed by multisubunit circular protein oligomers whose internal geometry has evolved to meet functional requirements. The subunit number is arguably the most critical parameter of a circular protein assembly, affecting the internal and external diameters of the assembly and often impacting on the protein's function. Although accurate structural information has been obtained for several circular proteins, a lack of accurate information on alternative oligomeric states has prevented engineering such transitions. In this study we used the bacterial transcription regulator TRAP as a model system to investigate the features that define the oligomeric state of a circular protein and to question how the subunit number could be manipulated.

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Organizational Affiliation: 

York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C12  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 45.3 kDa 
• Atom Count: 3,634 
• Modelled Residue Count: 390 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION ATTENUATION PROTEIN MTRB	A, B, C, D, E, F	65	Bacillus subtilis	Mutation(s): 0
UniProt
Find proteins for P19466 (Bacillus subtilis (strain 168)) Explore P19466  Go to UniProtKB:  P19466

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRP	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.348	α = 90
b = 146.348	β = 90
c = 146.348	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Chen, C., Smits, C., Dodson, G.G., Shevtsov, M.B., Merlino, N., Gollnick, P., Antson, A.A.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2011-10-26
  Changes: Database references
• Version 1.2: 2016-10-19
  Changes: Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description