5V76 | pdb_00005v76

Structure of Haliangium ochraceum BMC-T HO-3341

• PDB DOI: https://doi.org/10.2210/pdb5V76/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Haliangium ochraceum DSM 14365
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-17 Released: 2017-06-21 
• Deposition Author(s): Sutter, M., Paasch, B., Zarzycki, J., Aussignargues, C., Kerfeld, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.171 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell.

Sutter, M., Greber, B., Aussignargues, C., Kerfeld, C.A.

(2017) Science 356: 1293-1297

• PubMed: 28642439 
• DOI: https://doi.org/10.1126/science.aan3289
• Primary Citation Related Structures: 
  5V74, 5V75, 5V76


• PubMed Abstract: 
  

  Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable protein shell; prominent examples include the carboxysome for CO ₂ fixation and catabolic microcompartments found in many pathogenic microbes. The shell sequesters enzymatic reactions from the cytosol, analogous to the lipid-based membrane of eukaryotic organelles. Despite available structural information for single building blocks, the principles of shell assembly have remained elusive. We present the crystal structure of an intact shell from Haliangium ochraceum , revealing the basic principles of bacterial microcompartment shell construction. Given the conservation among shell proteins of all bacterial microcompartments, these principles apply to functionally diverse organelles and can inform the design and engineering of shells with new functionalities.

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Organizational Affiliation: 
• Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA. [e-mail].
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.84 kDa 
• Atom Count: 3,504 
• Modeled Residue Count: 412 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcompartments protein	A, B	206	Haliangium ochraceum DSM 14365	Mutation(s): 0  Gene Names: Hoch_3341
UniProt
Find proteins for D0LV02 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2)) Explore D0LV02  Go to UniProtKB:  D0LV02

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.171 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.571	α = 90
b = 110.571	β = 90
c = 110.571	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Sutter, M., Paasch, B., Zarzycki, J., Aussignargues, C., Kerfeld, C.A.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description