6EYH | pdb_00006eyh

Structure of a OpuBC mutant with bound Glycine betaine

• PDB DOI: https://doi.org/10.2210/pdb6EYH/pdb

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


• Deposited: 2017-11-13 Released: 2018-11-21 
• Deposition Author(s): Peherstorfer, S., Teichmann, L., Smits, S.H., Schmitt, L., Bremer, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structure of a OpuBC mutant with bound DMSP

Peherstorfer, S., Teichmann, L., Smits, S.H., Schmitt, L., Bremer, E.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.57 kDa 
• Atom Count: 2,607 
• Modeled Residue Count: 280 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline binding protein OpuBC	A	306	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0
UniProt
Find proteins for Q45462 (Bacillus subtilis (strain 168)) Explore Q45462  Go to UniProtKB:  Q45462

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DQY	B [auth A]	3-(dimethyl-lambda~4~-sulfanyl)propanoic acid C5 H12 O2 S BBSYGEAKHYDEGI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.77	α = 90
b = 65.89	β = 92.14
c = 63.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Peherstorfer, S., Teichmann, L., Smits, S.H., Schmitt, L., Bremer, E.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description