6XPL | pdb_00006xpl

CutR Screw, form 2 with 33.8 angstrom pitch

• PDB DOI: https://doi.org/10.2210/pdb6XPL/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Streptococcus intermedius SK54 = ATCC 27335
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-08 Released: 2020-07-22 
• Deposition Author(s): Ochoa, J.M., Sawaya, M.R., Nguyen, V.N., Duilio, C., Yeates, T.O.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.265 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.205 (DCC) 

Starting Model: experimental

Literature

Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization.

Ochoa, J.M., Nguyen, V.N., Nie, M., Sawaya, M.R., Bobik, T.A., Yeates, T.O.

(2020) Protein Sci 29: 2201-2212

• PubMed: 32885887 
• DOI: https://doi.org/10.1002/pro.3941
• Primary Citation Related Structures: 
  6XPH, 6XPI, 6XPJ, 6XPK, 6XPL


• PubMed Abstract: 
  

  Bacterial microcompartments are protein-based organelles that carry out specialized metabolic functions in diverse bacteria. Their outer shells are built from several thousand protein subunits. Some of the architectural principles of bacterial microcompartments have been articulated, with lateral packing of flat hexameric BMC proteins providing the basic foundation for assembly. Nonetheless, a complete understanding has been elusive, partly owing to polymorphic mechanisms of assembly exhibited by most microcompartment types. An earlier study of one homologous BMC shell protein subfamily, EutS/PduU, revealed a profoundly bent, rather than flat, hexameric structure. The possibility of a specialized architectural role was hypothesized, but artifactual effects of crystallization could not be ruled out. Here we report a series of crystal structures of an orthologous protein, CutR, from a glycyl-radical type choline-utilizing microcompartment from the bacterium Streptococcus intermedius. Depending on crystal form, expression construct, and minor mutations, a range of novel quaternary architectures was observed, including two spiral hexagonal assemblies. A new graphical approach helps illuminate the variations in BMC hexameric structure, with results substantiating the idea that the EutS/PduU/CutR subfamily of BMC proteins may endow microcompartment shells with flexible modes of assembly.

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Organizational Affiliation: 
• UCLA-Molecular Biology Institute, University of California, Los Angeles (UCLA), California, Los Angeles, USA.
Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA.
UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles (UCLA), California, Los Angeles, USA.
Department of Biochemistry, Biophysics and Molecular Biology; Iowa State University, Ames, Iowa, USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.28 kDa 
• Atom Count: 720 
• Modeled Residue Count: 98 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethanolamine utilization protein EutS	A	123	Streptococcus intermedius SK54 = ATCC 27335	Mutation(s): 0  Gene Names: HMPREF1654_00416
UniProt
Find proteins for A0A0E2IV13 (Streptococcus intermedius (strain ATCC 27335 / DSM 20573 / CCUG 32759 / CIP 103248 / JCM 12996 / LMG 17840 / NCTC 11324 / SK54 / 1877)) Explore A0A0E2IV13  Go to UniProtKB:  A0A0E2IV13

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.265 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.205 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.91	α = 90
b = 64.91	β = 90
c = 33.78	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Ochoa, J.M., Sawaya, M.R., Nguyen, V.N., Duilio, C., Yeates, T.O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references
• Version 1.2: 2020-11-11
  Changes: Database references
• Version 1.3: 2021-06-30
  Changes: Data collection
• Version 1.4: 2023-10-18
  Changes: Data collection, Database references, Refinement description