3RIO | pdb_00003rio

Crystal structure of GlcT CAT-PRDI

• PDB DOI: https://doi.org/10.2210/pdb3RIO/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-14 Released: 2012-05-09 
• Deposition Author(s): Himmel, S., Grosse, C., Wolff, S., Becker, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.246 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Structure of the RBD-PRDI fragment of the antiterminator protein GlcT.

Himmel, S., Grosse, C., Wolff, S., Schwiegk, C., Becker, S.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 751-756

• PubMed: 22750856 
• DOI: https://doi.org/10.1107/S1744309112020635
• Primary Citation Related Structures: 
  3RIO


• PubMed Abstract: 
  

  GlcT is a transcriptional antiterminator protein that is involved in regulation of glucose metabolism in Bacillus subtilis. Antiterminator proteins bind specific RNA sequences, thus preventing the formation of overlapping terminator stem-loops. The structure of a fragment (residues 3-170) comprising the RNA-binding domain (RBD) and the first regulatory domain (PRDI) of GlcT was solved at 2.0 Å resolution with one molecule in the asymmetric unit. The two domains are connected by a helical linker. Their interface is mostly constituted by hydrophobic interactions.

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Organizational Affiliation: 
• Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 21.19 kDa 
• Atom Count: 1,496 
• Modeled Residue Count: 168 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PtsGHI operon antiterminator	A	180	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU13880, glcT, ykwA
UniProt
Find proteins for O31691 (Bacillus subtilis (strain 168)) Explore O31691  Go to UniProtKB:  O31691

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.246 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.755	α = 90
b = 47.597	β = 90
c = 126.779	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
BUSTER	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Himmel, S., Grosse, C., Wolff, S., Becker, S.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-07-11
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations